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# Set seed for reproducibility
set.seed(42)
# Load required libraries for DESeq2 analysis and visualization
library(DESeq2)
library(SummarizedExperiment)
library(ggplot2)
library(pheatmap)
library(RColorBrewer)
library(ggrepel)
library(tidyverse)
library(VennDiagram)
library(gridExtra)
library(BiocParallel)
library(gt)
library(broom)
library(car)
library(emmeans)
library(multcomp)
library(MASS)
library(rstatix)
library(coin)
# Load libraries for enrichment analysis
library(clusterProfiler)
library(org.Dr.eg.db)
library(AnnotationDbi)
library(furrr)
# Define treatment order and color palette for plotting (original naming convention)
treatment_order_plot <- c(
"A- T- P-", # Control
"A- T- P+", # Parasite
"A+ T- P-", # Antibiotics
"A+ T- P+", # Antibiotics_Parasite
"A- T+ P-", # Temperature
"A- T+ P+", # Temperature_Parasite
"A+ T+ P-", # Antibiotics_Temperature
"A+ T+ P+" # Antibiotics_Temperature_Parasite
)
# Custom color palette matching treatment order
treatment_colors <- c(
"#1B9E77", # A- T- P- (Control)
"#D95F02", # A- T- P+ (Parasite)
"#7570B3", # A+ T- P- (Antibiotics)
"#E7298A", # A+ T- P+ (Antibiotics_Parasite)
"#66A61E", # A- T+ P- (Temperature)
"#E6AB02", # A- T+ P+ (Temperature_Parasite)
"#A6761D", # A+ T+ P- (Antibiotics_Temperature)
"#666666" # A+ T+ P+ (Antibiotics_Temperature_Parasite)
)
# Create named vector for color scale
treatment_color_scale <- setNames(treatment_colors, treatment_order_plot)
# Define treatment order for DESeq2 (keep original DESeq2-compatible names)
treatment_order_deseq <- c(
"A_minus_T_minus_P_minus", # Control
"A_minus_T_minus_P_plus", # Parasite
"A_plus_T_minus_P_minus", # Antibiotics
"A_plus_T_minus_P_plus", # Antibiotics_Parasite
"A_minus_T_plus_P_minus", # Temperature
"A_minus_T_plus_P_plus", # Temperature_Parasite
"A_plus_T_plus_P_minus", # Antibiotics_Temperature
"A_plus_T_plus_P_plus" # Antibiotics_Temperature_Parasite
)
# Create mapping between DESeq2 names and plotting names
treatment_mapping <- setNames(treatment_order_plot, treatment_order_deseq)
# Mapping from DESeq2 contrast names to plotting-friendly names
contrast_to_plotname <- c(
"A_minus_T_minus_P_minus_vs_A_minus_T_minus_P_minus" = "A- T- P-",
"A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus" = "A- T- P+",
"A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus" = "A+ T- P-",
"A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_minus" = "A+ T- P+",
"A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus" = "A- T+ P-",
"A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_minus" = "A- T+ P+",
"A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus" = "A+ T+ P-",
"A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_minus" = "A+ T+ P+"
)
# Function to convert DESeq2 treatment names to plotting names
convert_treatment_names <- function(deseq_names) {
return(treatment_mapping[deseq_names])
}
# Function to monitor system resources during analysis
monitor_performance <- function() {
# Get memory usage
mem_usage <- gc()
# Get CPU usage (if possible)
cpu_info <- tryCatch({
if (Sys.info()["sysname"] == "Darwin") {
# macOS
cpu_cmd <- "top -l 1 -n 0 | grep 'CPU usage'"
cpu_output <- system(cpu_cmd, intern = TRUE)
cpu_output
} else if (Sys.info()["sysname"] == "Linux") {
# Linux
cpu_cmd <- "top -bn1 | grep 'Cpu(s)'"
cpu_output <- system(cpu_cmd, intern = TRUE)
cpu_output
} else {
"CPU monitoring not available on this system"
}
}, error = function(e) {
"CPU monitoring not available"
})
cat("=== Performance Monitor ===\n")
cat("Memory usage:\n")
print(mem_usage)
cat("CPU info:\n")
cat(cpu_info, "\n")
cat("Active parallel workers:", bp_param$workers, "\n")
cat("========================\n")
}
# Function to optimize memory usage
optimize_memory <- function() {
cat("Optimizing memory usage...\n")
# Force garbage collection
gc(verbose = FALSE)
# Clear unnecessary objects
if (exists("temp_objects")) {
rm(temp_objects)
}
cat("Memory optimization complete\n")
}
# Function to save DESeq2 results
save_deseq_results <- function(results_list, analysis_name) {
# Create results directory if it doesn't exist
results_dir <- here::here("Code", "Analysis", "DiffExpGene", "Saved_Results")
dir.create(results_dir, recursive = TRUE, showWarnings = FALSE)
# Save the results list
results_file <- file.path(results_dir, paste0(analysis_name, "_deseq_results.rds"))
saveRDS(results_list, results_file)
cat("Results saved to:", results_file, "\n")
}
# Function to load DESeq2 results
load_deseq_results <- function(analysis_name) {
results_dir <- here::here("Code", "Analysis", "DiffExpGene", "Saved_Results")
results_file <- file.path(results_dir, paste0(analysis_name, "_deseq_results.rds"))
if (file.exists(results_file)) {
cat("Loading existing results for:", analysis_name, "\n")
return(readRDS(results_file))
} else {
cat("No existing results found for:", analysis_name, "\n")
return(NULL)
}
}
# Function to check if results exist
results_exist <- function(analysis_name) {
results_dir <- here::here("Code", "Analysis", "DiffExpGene", "Saved_Results")
results_file <- file.path(results_dir, paste0(analysis_name, "_deseq_results.rds"))
return(file.exists(results_file))
}
# Function to clean up saved results
cleanup_saved_results <- function(analysis_names = NULL) {
results_dir <- here::here("Code", "Analysis", "DiffExpGene", "Saved_Results")
if (is.null(analysis_names)) {
# Remove all saved results
if (dir.exists(results_dir)) {
unlink(results_dir, recursive = TRUE)
cat("All saved results removed\n")
}
} else {
# Remove specific analysis results
for (analysis_name in analysis_names) {
results_file <- file.path(results_dir, paste0(analysis_name, "_deseq_results.rds"))
if (file.exists(results_file)) {
file.remove(results_file)
cat("Removed saved results for:", analysis_name, "\n")
}
}
}
}
# Function to run DESeq2 analysis for a single comparison
run_deseq_comparison <- function(dds, contrast_name, contrast_vector) {
cat("Running analysis for:", contrast_name, "\n")
# Set seed for reproducibility within parallel processes
set.seed(42)
# Optimize DESeq2 settings for speed
# Use faster estimation method for large datasets
if (nrow(dds) > 10000) {
# For large datasets, use faster estimation
dds_comparison <- DESeq(dds,
parallel = TRUE,
fitType = "local", # Faster than "parametric"
betaPrior = FALSE, # Disable beta prior for speed
quiet = FALSE)
} else {
# For smaller datasets, use standard settings
dds_comparison <- DESeq(dds,
parallel = TRUE,
quiet = FALSE)
}
# Get results with optimized settings
res_comparison <- results(dds_comparison,
contrast = contrast_vector,
parallel = TRUE,
alpha = 0.05) # Set significance threshold
# Add gene names if available
if ("gene_name" %in% names(mcols(dds_comparison))) {
res_comparison$gene_name <- mcols(dds_comparison)$gene_name
}
# Clean up memory
rm(dds_comparison)
gc()
return(res_comparison)
}
# Function to run all comparisons for a specific analysis with enhanced parallelization
run_analysis_set <- function(analysis_name, analysis_config, force_recompute = FALSE) {
cat("\n=== Running", analysis_name, "===\n")
cat("Description:", analysis_config$description, "\n")
# Check if results already exist and force_recompute is FALSE
if (!force_recompute && results_exist(analysis_name)) {
cat("Loading existing results for", analysis_name, "\n")
return(load_deseq_results(analysis_name))
}
# Create a copy of the dataset for this analysis
dds_analysis <- dds_filtered
# Update design if needed
design(dds_analysis) <- analysis_config$design
# Pre-estimate size factors and dispersions for better parallelization
cat("Pre-estimating size factors and dispersions...\n")
dds_analysis <- estimateSizeFactors(dds_analysis)
dds_analysis <- estimateDispersions(dds_analysis)
# Run all contrasts for this analysis
results_list <- list()
# Use parallel processing for multiple contrasts
if (length(analysis_config$contrasts) > 1) {
cat("Running", length(analysis_config$contrasts), "contrasts in parallel...\n")
# Create a function for parallel execution
run_single_contrast <- function(contrast_info) {
contrast_name <- contrast_info$name
contrast_vector <- contrast_info$vector
# Check if both treatment levels exist in the data
if (all(contrast_vector[2:3] %in% levels(colData(dds_analysis)$Treatment))) {
return(list(name = contrast_name, result = run_deseq_comparison(dds_analysis, contrast_name, contrast_vector)))
} else {
cat("Warning: Contrast", contrast_name, "skipped - treatment levels not found in data\n")
return(list(name = contrast_name, result = NULL))
}
}
# Prepare contrast information for parallel processing
contrast_info_list <- lapply(names(analysis_config$contrasts), function(name) {
list(name = name, vector = analysis_config$contrasts[[name]])
})
# Run contrasts in parallel
parallel_results <- BiocParallel::bplapply(contrast_info_list, run_single_contrast)
# Organize results
for (result in parallel_results) {
if (!is.null(result$result)) {
results_list[[result$name]] <- result$result
}
}
} else {
# For single contrast, run directly
for (contrast_name in names(analysis_config$contrasts)) {
contrast_vector <- analysis_config$contrasts[[contrast_name]]
# Check if both treatment levels exist in the data
if (all(contrast_vector[2:3] %in% levels(colData(dds_analysis)$Treatment))) {
results_list[[contrast_name]] <- run_deseq_comparison(dds_analysis, contrast_name, contrast_vector)
} else {
cat("Warning: Contrast", contrast_name, "skipped - treatment levels not found in data\n")
}
}
}
# Save the results
save_deseq_results(results_list, analysis_name)
# Clean up memory
rm(dds_analysis)
gc()
return(results_list)
}
# Function to format p-values for gt tables
fmt_pvalues <- function(gt_tbl, columns, threshold = 0.001, decimals = 3) {
gt_tbl |>
gt::fmt_number(columns = all_of(columns), decimals = decimals) |>
gt::fmt(
columns = all_of(columns),
rows = Reduce(`|`, lapply(columns, function(col) gt_tbl$`_data`[[col]] < threshold)),
fns = function(x) rep(paste0("<", threshold), length(x))
)
}
# Function to save results for each analysis
save_analysis_results <- function(analysis_name, results_list) {
cat("Saving results for:", analysis_name, "\n")
# Create subdirectory for this analysis
analysis_dir <- file.path(output_dir, analysis_name)
dir.create(analysis_dir, recursive = TRUE, showWarnings = FALSE)
# Save each contrast result
for (contrast_name in names(results_list)) {
res <- results_list[[contrast_name]]
# Convert to data frame
res_df <- as.data.frame(res) %>% rownames_to_column(var = "gene")
# Add gene names if available
if ("gene_name" %in% names(res_df)) {
res_df <- res_df %>%
dplyr::select(gene_name, everything()) %>%
dplyr::rename(gene = gene_name)
}
# Save full results
full_filename <- file.path(analysis_dir, paste0(contrast_name, "_full_results.tsv"))
write_tsv(res_df, full_filename)
# Save significant results (padj < 0.05)
sig_df <- res_df %>%
dplyr::filter(padj < 0.05) %>%
dplyr::arrange(padj)
if (nrow(sig_df) > 0) {
sig_filename <- file.path(analysis_dir, paste0(contrast_name, "_significant_results.tsv"))
write_tsv(sig_df, sig_filename)
# Create summary table
summary_table <- data.frame(
Contrast = contrast_name,
Total_Genes = nrow(res_df),
Significant_Genes = nrow(sig_df),
Upregulated = sum(sig_df$log2FoldChange > 0, na.rm = TRUE),
Downregulated = sum(sig_df$log2FoldChange < 0, na.rm = TRUE),
stringsAsFactors = FALSE
)
# Save summary
summary_filename <- file.path(analysis_dir, paste0(contrast_name, "_summary.tsv"))
write_tsv(summary_table, summary_filename)
}
}
# Create combined summary for the analysis
all_summaries <- list()
for (contrast_name in names(results_list)) {
res <- results_list[[contrast_name]]
res_df <- as.data.frame(res)
sig_df <- res_df %>% dplyr::filter(padj < 0.05)
all_summaries[[contrast_name]] <- data.frame(
Contrast = contrast_name,
Total_Genes = nrow(res_df),
Significant_Genes = nrow(sig_df),
Upregulated = sum(sig_df$log2FoldChange > 0, na.rm = TRUE),
Downregulated = sum(sig_df$log2FoldChange < 0, na.rm = TRUE),
stringsAsFactors = FALSE
)
}
combined_summary <- bind_rows(all_summaries)
combined_filename <- file.path(analysis_dir, paste0(analysis_name, "_combined_summary.tsv"))
write_tsv(combined_summary, combined_filename)
# Display summary table
cat("\nSummary for", analysis_name, ":\n")
print(combined_summary %>% gt::gt())
}
# Function to convert gene IDs to Entrez IDs for enrichment analysis
get_entrez_ids <- function(deg_df) {
# Set seed for reproducibility
set.seed(42)
# Use org.Dr.eg.db to map gene symbols to Entrez IDs
gene_ids <- deg_df$gene
# Create a mapping dataframe
entrez_map <- AnnotationDbi::mapIds(
org.Dr.eg.db,
keys = gene_ids,
column = "ENTREZID",
keytype = "SYMBOL",
multiVals = "first"
) %>%
tibble::enframe(name = "gene", value = "entrezgene_id") %>%
dplyr::filter(!is.na(entrezgene_id))
# Join with original data to keep all information
result <- deg_df %>%
dplyr::left_join(entrez_map, by = "gene") %>%
dplyr::filter(!is.na(entrezgene_id)) %>%
dplyr::distinct(entrezgene_id, .keep_all = TRUE)
return(result)
}
# Function to perform GO enrichment analysis
perform_go_enrichment <- function(entrez_df, contrast_name) {
# Set seed for reproducibility
set.seed(42)
cat("Performing GO enrichment for:", contrast_name, "\n")
cat("Number of genes:", nrow(entrez_df), "\n")
# Perform GO enrichment
go_results <- clusterProfiler::enrichGO(
gene = entrez_df$entrezgene_id,
OrgDb = org.Dr.eg.db,
keyType = "ENTREZID",
ont = "BP", # Biological Process
pAdjustMethod = "BH",
pvalueCutoff = 0.1,
readable = TRUE
) %>%
as.data.frame() %>%
dplyr::select(Description, p.adjust, Count, geneID) %>%
dplyr::mutate(log_padj = -log10(p.adjust))
# Create a mapping of gene symbols to Entrez IDs
symbol_to_entrez <- AnnotationDbi::mapIds(
org.Dr.eg.db,
keys = entrez_df$entrezgene_id,
column = "SYMBOL",
keytype = "ENTREZID",
multiVals = "first"
) %>%
tibble::enframe(name = "entrezgene_id", value = "SYMBOL") %>%
dplyr::filter(!is.na(SYMBOL))
# Create a mapping of gene IDs to log2FoldChange
gene_fc_map <- entrez_df %>%
dplyr::select(entrezgene_id, log2FoldChange) %>%
dplyr::left_join(symbol_to_entrez, by = "entrezgene_id") %>%
dplyr::select(SYMBOL, log2FoldChange) %>%
dplyr::filter(!is.na(SYMBOL))
# Split the geneID column and create a long format dataframe
go_results_long <- go_results %>%
tidyr::separate_rows(geneID, sep = "/") %>%
# Join with the fold change data using gene symbols
dplyr::left_join(gene_fc_map, by = c("geneID" = "SYMBOL"))
# Group back by GO term and calculate summary statistics
go_results_summary <- go_results_long %>%
dplyr::group_by(Description, p.adjust, Count, log_padj) %>%
dplyr::summarise(
mean_log2FC = mean(log2FoldChange, na.rm = TRUE),
n_up = sum(log2FoldChange > 0, na.rm = TRUE),
n_down = sum(log2FoldChange < 0, na.rm = TRUE),
gene_list = list(geneID),
fc_list = list(log2FoldChange),
.groups = "drop"
)
return(go_results_summary)
}
# Function to perform KEGG enrichment analysis
perform_kegg_enrichment <- function(entrez_df, contrast_name) {
# Set seed for reproducibility
set.seed(42)
cat("Performing KEGG enrichment for:", contrast_name, "\n")
cat("Number of genes:", nrow(entrez_df), "\n")
# Perform KEGG enrichment
kegg_results <- clusterProfiler::enrichKEGG(
gene = entrez_df$entrezgene_id,
organism = 'dre', # Danio rerio
keyType = 'ncbi-geneid',
pvalueCutoff = 0.1,
pAdjustMethod = "BH"
) %>%
as.data.frame() %>%
dplyr::select(Description, p.adjust, Count, geneID) %>%
dplyr::mutate(log_padj = -log10(p.adjust))
# Create a mapping of gene IDs to log2FoldChange
gene_fc_map <- entrez_df %>%
dplyr::select(entrezgene_id, log2FoldChange) %>%
dplyr::mutate(entrezgene_id = as.character(entrezgene_id))
# Split the geneID column and create a long format dataframe
kegg_results_long <- kegg_results %>%
tidyr::separate_rows(geneID, sep = "/") %>%
# Convert geneID to character for joining
dplyr::mutate(geneID = as.character(geneID)) %>%
# Join with the fold change data
dplyr::left_join(gene_fc_map, by = c("geneID" = "entrezgene_id"))
# Group back by KEGG pathway and calculate summary statistics
kegg_results_summary <- kegg_results_long %>%
dplyr::group_by(Description, p.adjust, Count, log_padj) %>%
dplyr::summarise(
mean_log2FC = mean(log2FoldChange, na.rm = TRUE),
n_up = sum(log2FoldChange > 0, na.rm = TRUE),
n_down = sum(log2FoldChange < 0, na.rm = TRUE),
gene_list = list(geneID),
fc_list = list(log2FoldChange),
.groups = "drop"
)
return(kegg_results_summary)
}
# Function to prepare data for enrichment heatmaps
prepare_enrichment_heatmap <- function(enrichment_results, top_n = 15) {
# Get top terms from each contrast
top_terms <- enrichment_results %>%
purrr::map(~ dplyr::slice_max(.x, order_by = log_padj, n = top_n)) %>%
purrr::map(~ dplyr::pull(.x, Description)) %>%
unlist() %>%
unique()
# Create matrix for heatmap
heatmap_data <- enrichment_results %>%
purrr::map_dfr(~ dplyr::filter(.x, Description %in% top_terms), .id = "contrast") %>%
# Convert contrast names to readable format
dplyr::mutate(contrast = purrr::map_chr(contrast, convert_contrast_names)) %>%
tidyr::pivot_wider(
id_cols = Description,
names_from = contrast,
values_from = log_padj,
values_fill = 0
) %>%
tibble::column_to_rownames("Description") %>%
as.matrix()
return(heatmap_data)
}
# Function to prepare data for regulation heatmaps
prepare_regulation_heatmap <- function(enrichment_results, direction = "up", top_n = 20) {
# Combine all results
all_results <- purrr::map_dfr(enrichment_results, ~.x, .id = "contrast")
# Convert contrast names to readable format
all_results <- all_results %>%
dplyr::mutate(contrast = purrr::map_chr(contrast, convert_contrast_names))
# Filter for terms with significant regulation in the specified direction
filtered_terms <- all_results %>%
dplyr::filter(
if(direction == "up") {
n_up > n_down
} else {
n_down > n_up
}
) %>%
dplyr::group_by(Description) %>%
dplyr::summarise(
total_terms = n(),
mean_fc = mean(mean_log2FC, na.rm = TRUE),
.groups = "drop"
) %>%
dplyr::arrange(desc(total_terms)) %>%
dplyr::slice_head(n = top_n)
# Create heatmap data
heatmap_data <- all_results %>%
dplyr::filter(Description %in% filtered_terms$Description) %>%
dplyr::select(contrast, Description, mean_log2FC) %>%
tidyr::pivot_wider(
names_from = contrast,
values_from = mean_log2FC,
values_fill = 0
) %>%
tibble::column_to_rownames("Description")
# Set color scheme based on direction
if(direction == "up") {
color_scheme <- colorRampPalette(c("white", "red"))(100)
# For up-regulated, we want to show the magnitude of positive changes
heatmap_data[heatmap_data < 0] <- 0
} else {
color_scheme <- colorRampPalette(c("white", "blue"))(100)
# For down-regulated, we want to show the magnitude of negative changes
heatmap_data[heatmap_data > 0] <- 0
# Make negative values positive for visualization
heatmap_data <- abs(heatmap_data)
}
return(list(heatmap_data = heatmap_data, color_scheme = color_scheme))
}
# Function to run enrichment analysis for a specific analysis
run_enrichment_analysis <- function(analysis_name, results_list) {
cat("\n=== Running Enrichment Analysis for:", analysis_name, "===\n")
# Convert results to tidy format and filter significant genes
contrast_tibbles <- purrr::map(results_list, ~
as.data.frame(.) %>%
tibble::rownames_to_column("gene") %>%
dplyr::filter(
padj < 0.05,
abs(log2FoldChange) > 1,
!gene %in% genes_to_exclude # Filter out excluded genes
) %>%
dplyr::select(gene, log2FoldChange, padj)
)
# Convert to Entrez IDs
entrez_by_contrast <- purrr::map(contrast_tibbles, get_entrez_ids)
# Run GO enrichment
cat("Running GO enrichment...\n")
go_by_contrast <- purrr::map2(entrez_by_contrast, names(entrez_by_contrast),
perform_go_enrichment)
names(go_by_contrast) <- names(entrez_by_contrast)
# Run KEGG enrichment
cat("Running KEGG enrichment...\n")
kegg_by_contrast <- purrr::map2(entrez_by_contrast, names(entrez_by_contrast),
perform_kegg_enrichment)
names(kegg_by_contrast) <- names(entrez_by_contrast)
return(list(
go_results = go_by_contrast,
kegg_results = kegg_by_contrast,
entrez_data = entrez_by_contrast
))
}
# Function to convert DESeq2 contrast names to readable format
convert_contrast_names <- function(contrast_name) {
# Define mapping for common contrast patterns
contrast_mapping <- c(
"A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus" = "A- T- P+ vs A- T- P-",
"A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus" = "A+ T- P- vs A- T- P-",
"A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_minus" = "A+ T- P+ vs A- T- P-",
"A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus" = "A- T+ P- vs A- T- P-",
"A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_minus" = "A- T+ P+ vs A- T- P-",
"A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus" = "A+ T+ P- vs A- T- P-",
"A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_minus" = "A+ T+ P+ vs A- T- P-",
"A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_plus" = "A+ T- P+ vs A- T- P+",
"A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_plus" = "A- T+ P+ vs A- T- P+",
"A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_plus" = "A+ T+ P+ vs A- T- P+"
)
# Check if the contrast name is in our mapping
if (contrast_name %in% names(contrast_mapping)) {
return(contrast_mapping[contrast_name])
} else {
# If not in mapping, try to convert using pattern matching
# Replace underscores with spaces and convert to readable format
readable_name <- contrast_name %>%
stringr::str_replace_all("_minus", "-") %>%
stringr::str_replace_all("_plus", "+") %>%
stringr::str_replace_all("_vs_", " vs ") %>%
stringr::str_replace_all("A", "A") %>%
stringr::str_replace_all("T", "T") %>%
stringr::str_replace_all("P", "P")
return(readable_name)
}
}
# Function to save enrichment results
save_enrichment_results <- function(enrichment_results, analysis_name) {
cat("Saving enrichment results for:", analysis_name, "\n")
# Create subdirectory for this analysis
analysis_dir <- file.path(output_dir, analysis_name, "enrichment")
dir.create(analysis_dir, recursive = TRUE, showWarnings = FALSE)
# Save individual contrast GO results (all terms, not just top)
for (contrast_name in names(enrichment_results$go_results)) {
go_res <- enrichment_results$go_results[[contrast_name]]
if (nrow(go_res) > 0) {
# Save all GO results for this contrast
go_filename <- file.path(analysis_dir, paste0(contrast_name, "_GO_enrichment_ALL.tsv"))
write_tsv(go_res, go_filename)
# Also save top 20 for quick reference
go_top20 <- go_res %>% dplyr::slice_max(order_by = log_padj, n = 20)
go_top20_filename <- file.path(analysis_dir, paste0(contrast_name, "_GO_enrichment_TOP20.tsv"))
write_tsv(go_top20, go_top20_filename)
}
}
# Save individual contrast KEGG results (all pathways, not just top)
for (contrast_name in names(enrichment_results$kegg_results)) {
kegg_res <- enrichment_results$kegg_results[[contrast_name]]
if (nrow(kegg_res) > 0) {
# Save all KEGG results for this contrast
kegg_filename <- file.path(analysis_dir, paste0(contrast_name, "_KEGG_enrichment_ALL.tsv"))
write_tsv(kegg_res, kegg_filename)
# Also save top 20 for quick reference
kegg_top20 <- kegg_res %>% dplyr::slice_max(order_by = log_padj, n = 20)
kegg_top20_filename <- file.path(analysis_dir, paste0(contrast_name, "_KEGG_enrichment_TOP20.tsv"))
write_tsv(kegg_top20, kegg_top20_filename)
}
}
# Save combined summary (all results across contrasts)
if (length(enrichment_results$go_results) > 0) {
go_summary <- purrr::map_dfr(enrichment_results$go_results, ~.x, .id = "contrast")
go_summary_filename <- file.path(analysis_dir, paste0(analysis_name, "_GO_summary_ALL.tsv"))
write_tsv(go_summary, go_summary_filename)
# Save top 50 GO terms across all contrasts
go_top50 <- go_summary %>%
dplyr::slice_max(order_by = log_padj, n = 50)
go_top50_filename <- file.path(analysis_dir, paste0(analysis_name, "_GO_summary_TOP50.tsv"))
write_tsv(go_top50, go_top50_filename)
}
if (length(enrichment_results$kegg_results) > 0) {
kegg_summary <- purrr::map_dfr(enrichment_results$kegg_results, ~.x, .id = "contrast")
kegg_summary_filename <- file.path(analysis_dir, paste0(analysis_name, "_KEGG_summary_ALL.tsv"))
write_tsv(kegg_summary, kegg_summary_filename)
# Save top 50 KEGG pathways across all contrasts
kegg_top50 <- kegg_summary %>%
dplyr::slice_max(order_by = log_padj, n = 50)
kegg_top50_filename <- file.path(analysis_dir, paste0(analysis_name, "_KEGG_summary_TOP50.tsv"))
write_tsv(kegg_top50, kegg_top50_filename)
}
# Save significant results only (padj < 0.05)
if (length(enrichment_results$go_results) > 0) {
go_significant <- purrr::map_dfr(enrichment_results$go_results, ~.x, .id = "contrast") %>%
dplyr::filter(p.adjust < 0.05)
if (nrow(go_significant) > 0) {
go_sig_filename <- file.path(analysis_dir, paste0(analysis_name, "_GO_significant.tsv"))
write_tsv(go_significant, go_sig_filename)
}
}
if (length(enrichment_results$kegg_results) > 0) {
kegg_significant <- purrr::map_dfr(enrichment_results$kegg_results, ~.x, .id = "contrast") %>%
dplyr::filter(p.adjust < 0.05)
if (nrow(kegg_significant) > 0) {
kegg_sig_filename <- file.path(analysis_dir, paste0(analysis_name, "_KEGG_significant.tsv"))
write_tsv(kegg_significant, kegg_sig_filename)
}
}
# Create and save a comprehensive summary report
create_comprehensive_report(enrichment_results, analysis_name, analysis_dir)
cat("Enrichment results saved to:", analysis_dir, "\n")
}
# Function to create comprehensive enrichment report
create_comprehensive_report <- function(enrichment_results, analysis_name, analysis_dir) {
cat("Creating comprehensive report for:", analysis_name, "\n")
# Initialize report data
report_data <- list()
# GO analysis summary
if (length(enrichment_results$go_results) > 0) {
go_all <- purrr::map_dfr(enrichment_results$go_results, ~.x, .id = "contrast")
report_data$go_summary <- list(
total_terms = nrow(go_all),
significant_terms = sum(go_all$p.adjust < 0.05, na.rm = TRUE),
contrasts_analyzed = length(enrichment_results$go_results),
top_terms = go_all %>% dplyr::slice_max(order_by = log_padj, n = 10),
significant_terms_list = go_all %>% dplyr::filter(p.adjust < 0.05) %>% dplyr::arrange(p.adjust)
)
}
# KEGG analysis summary
if (length(enrichment_results$kegg_results) > 0) {
kegg_all <- purrr::map_dfr(enrichment_results$kegg_results, ~.x, .id = "contrast")
report_data$kegg_summary <- list(
total_pathways = nrow(kegg_all),
significant_pathways = sum(kegg_all$p.adjust < 0.05, na.rm = TRUE),
contrasts_analyzed = length(enrichment_results$kegg_results),
top_pathways = kegg_all %>% dplyr::slice_max(order_by = log_padj, n = 10),
significant_pathways_list = kegg_all %>% dplyr::filter(p.adjust < 0.05) %>% dplyr::arrange(p.adjust)
)
}
# Save comprehensive report as RDS
report_filename <- file.path(analysis_dir, paste0(analysis_name, "_comprehensive_report.rds"))
saveRDS(report_data, report_filename)
# Create and save a text summary
summary_text <- paste0(
"=== ENRICHMENT ANALYSIS REPORT ===\n",
"Analysis: ", analysis_name, "\n",
"Date: ", format(Sys.time(), "%Y-%m-%d %H:%M:%S"), "\n\n",
"GO ENRICHMENT SUMMARY:\n",
ifelse(length(enrichment_results$go_results) > 0,
paste0(" Total terms analyzed: ", report_data$go_summary$total_terms, "\n",
" Significant terms (padj < 0.05): ", report_data$go_summary$significant_terms, "\n",
" Contrasts analyzed: ", report_data$go_summary$contrasts_analyzed, "\n"),
" No GO results available\n"),
"\n",
"KEGG ENRICHMENT SUMMARY:\n",
ifelse(length(enrichment_results$kegg_results) > 0,
paste0(" Total pathways analyzed: ", report_data$kegg_summary$total_pathways, "\n",
" Significant pathways (padj < 0.05): ", report_data$kegg_summary$significant_pathways, "\n",
" Contrasts analyzed: ", report_data$kegg_summary$contrasts_analyzed, "\n"),
" No KEGG results available\n"),
"\n",
"FILES SAVED:\n",
" - Individual contrast files (ALL and TOP20)\n",
" - Combined summary files (ALL and TOP50)\n",
" - Significant results only (padj < 0.05)\n",
" - Comprehensive report (RDS format)\n",
" - This text summary\n"
)
summary_filename <- file.path(analysis_dir, paste0(analysis_name, "_analysis_summary.txt"))
writeLines(summary_text, summary_filename)
cat("Comprehensive report saved to:", report_filename, "\n")
cat("Text summary saved to:", summary_filename, "\n")
}
# Function to create combined enrichment summary across all analyses
create_combined_enrichment_summary <- function(enrichment_results) {
cat("Creating combined enrichment summary across all analyses...\n")
# Create combined directory
combined_dir <- file.path(output_dir, "Combined_Enrichment_Results")
dir.create(combined_dir, recursive = TRUE, showWarnings = FALSE)
# Combine all GO results
all_go_results <- list()
all_kegg_results <- list()
for (analysis_name in names(enrichment_results)) {
if (!is.null(enrichment_results[[analysis_name]]$go_results)) {
go_data <- purrr::map_dfr(enrichment_results[[analysis_name]]$go_results, ~.x, .id = "contrast") %>%
dplyr::mutate(analysis = analysis_name)
all_go_results[[analysis_name]] <- go_data
}
if (!is.null(enrichment_results[[analysis_name]]$kegg_results)) {
kegg_data <- purrr::map_dfr(enrichment_results[[analysis_name]]$kegg_results, ~.x, .id = "contrast") %>%
dplyr::mutate(analysis = analysis_name)
all_kegg_results[[analysis_name]] <- kegg_data
}
}
# Save combined GO results
if (length(all_go_results) > 0) {
combined_go <- dplyr::bind_rows(all_go_results) %>%
dplyr::arrange(analysis, contrast, desc(log_padj))
# Save all GO results
combined_go_filename <- file.path(combined_dir, "ALL_ANALYSES_GO_enrichment_ALL.tsv")
write_tsv(combined_go, combined_go_filename)
# Save top 100 GO terms across all analyses
combined_go_top100 <- combined_go %>%
dplyr::slice_max(order_by = log_padj, n = 100)
combined_go_top100_filename <- file.path(combined_dir, "ALL_ANALYSES_GO_enrichment_TOP100.tsv")
write_tsv(combined_go_top100, combined_go_top100_filename)
# Save significant GO terms only
combined_go_sig <- combined_go %>%
dplyr::filter(p.adjust < 0.05)
if (nrow(combined_go_sig) > 0) {
combined_go_sig_filename <- file.path(combined_dir, "ALL_ANALYSES_GO_enrichment_SIGNIFICANT.tsv")
write_tsv(combined_go_sig, combined_go_sig_filename)
}
cat("Combined GO results saved:\n")
cat(" - All results:", combined_go_filename, "\n")
cat(" - Top 100:", combined_go_top100_filename, "\n")
if (nrow(combined_go_sig) > 0) {
cat(" - Significant only:", combined_go_sig_filename, "\n")
}
}
# Save combined KEGG results
if (length(all_kegg_results) > 0) {
combined_kegg <- dplyr::bind_rows(all_kegg_results) %>%
dplyr::arrange(analysis, contrast, desc(log_padj))
# Save all KEGG results
combined_kegg_filename <- file.path(combined_dir, "ALL_ANALYSES_KEGG_enrichment_ALL.tsv")
write_tsv(combined_kegg, combined_kegg_filename)
# Save top 100 KEGG pathways across all analyses
combined_kegg_top100 <- combined_kegg %>%
dplyr::slice_max(order_by = log_padj, n = 100)
combined_kegg_top100_filename <- file.path(combined_dir, "ALL_ANALYSES_KEGG_enrichment_TOP100.tsv")
write_tsv(combined_kegg_top100, combined_kegg_top100_filename)
# Save significant KEGG pathways only
combined_kegg_sig <- combined_kegg %>%
dplyr::filter(p.adjust < 0.05)
if (nrow(combined_kegg_sig) > 0) {
combined_kegg_sig_filename <- file.path(combined_dir, "ALL_ANALYSES_KEGG_enrichment_SIGNIFICANT.tsv")
write_tsv(combined_kegg_sig, combined_kegg_sig_filename)
}
cat("Combined KEGG results saved:\n")
cat(" - All results:", combined_kegg_filename, "\n")
cat(" - Top 100:", combined_kegg_top100_filename, "\n")
if (nrow(combined_kegg_sig) > 0) {
cat(" - Significant only:", combined_kegg_sig_filename, "\n")
}
}
# Create comprehensive summary statistics
summary_stats <- list()
if (length(all_go_results) > 0) {
combined_go <- dplyr::bind_rows(all_go_results)
summary_stats$go <- list(
total_terms = nrow(combined_go),
significant_terms = sum(combined_go$p.adjust < 0.05, na.rm = TRUE),
analyses_count = length(all_go_results),
contrasts_count = length(unique(combined_go$contrast)),
top_terms = combined_go %>% dplyr::slice_max(order_by = log_padj, n = 20)
)
}
if (length(all_kegg_results) > 0) {
combined_kegg <- dplyr::bind_rows(all_kegg_results)
summary_stats$kegg <- list(
total_pathways = nrow(combined_kegg),
significant_pathways = sum(combined_kegg$p.adjust < 0.05, na.rm = TRUE),
analyses_count = length(all_kegg_results),
contrasts_count = length(unique(combined_kegg$contrast)),
top_pathways = combined_kegg %>% dplyr::slice_max(order_by = log_padj, n = 20)
)
}
# Save summary statistics
summary_stats_filename <- file.path(combined_dir, "ALL_ANALYSES_enrichment_summary_stats.rds")
saveRDS(summary_stats, summary_stats_filename)
# Create text summary
summary_text <- paste0(
"=== COMBINED ENRICHMENT ANALYSIS SUMMARY ===\n",
"Date: ", format(Sys.time(), "%Y-%m-%d %H:%M:%S"), "\n",
"Analyses included: ", paste(names(enrichment_results), collapse = ", "), "\n\n",
"GO ENRICHMENT SUMMARY:\n",
ifelse(length(all_go_results) > 0,
paste0(" Total terms analyzed: ", summary_stats$go$total_terms, "\n",
" Significant terms (padj < 0.05): ", summary_stats$go$significant_terms, "\n",
" Analyses included: ", summary_stats$go$analyses_count, "\n",
" Contrasts analyzed: ", summary_stats$go$contrasts_count, "\n"),
" No GO results available\n"),
"\n",
"KEGG ENRICHMENT SUMMARY:\n",
ifelse(length(all_kegg_results) > 0,
paste0(" Total pathways analyzed: ", summary_stats$kegg$total_pathways, "\n",
" Significant pathways (padj < 0.05): ", summary_stats$kegg$significant_pathways, "\n",
" Analyses included: ", summary_stats$kegg$analyses_count, "\n",
" Contrasts analyzed: ", summary_stats$kegg$contrasts_count, "\n"),
" No KEGG results available\n"),
"\n",
"FILES CREATED:\n",
" - ALL_ANALYSES_GO_enrichment_ALL.tsv (all GO results)\n",
" - ALL_ANALYSES_GO_enrichment_TOP100.tsv (top 100 GO terms)\n",
" - ALL_ANALYSES_GO_enrichment_SIGNIFICANT.tsv (significant GO terms only)\n",
" - ALL_ANALYSES_KEGG_enrichment_ALL.tsv (all KEGG results)\n",
" - ALL_ANALYSES_KEGG_enrichment_TOP100.tsv (top 100 KEGG pathways)\n",
" - ALL_ANALYSES_KEGG_enrichment_SIGNIFICANT.tsv (significant KEGG pathways only)\n",
" - ALL_ANALYSES_enrichment_summary_stats.rds (summary statistics)\n",
" - This text summary\n"
)
summary_filename <- file.path(combined_dir, "ALL_ANALYSES_enrichment_summary.txt")
writeLines(summary_text, summary_filename)
cat("\nCombined enrichment summary saved to:", combined_dir, "\n")
cat("Summary statistics saved to:", summary_stats_filename, "\n")
cat("Text summary saved to:", summary_filename, "\n")
}
# Read in metadata sheet
Metadata <- readxl::read_excel(here::here("Data", "Transcriptomics", "Data", "ROL_MajorExperiment__MetadataSheet__Corrected_05092025.xlsx"))
# Read in SummarizedExperiment object
se <- readRDS(here::here("Data", "Transcriptomics", "Results", "rnaseq", "051525", "salmon", "salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds"))
# Print basic information about the dataset
cat("Number of genes:", nrow(se), "\n")
## Number of genes: 39447
cat("Number of samples:", ncol(se), "\n")
## Number of samples: 72
cat("Sample names:", colnames(se), "\n")
## Sample names: TS047_RoL_RNA_110 TS047_RoL_RNA_112 TS047_RoL_RNA_114 TS047_RoL_RNA_116 TS047_RoL_RNA_119 TS047_RoL_RNA_136 TS047_RoL_RNA_142 TS047_RoL_RNA_145 TS047_RoL_RNA_146 TS047_RoL_RNA_16 TS047_RoL_RNA_170 TS047_RoL_RNA_175 TS047_RoL_RNA_177 TS047_RoL_RNA_20 TS047_RoL_RNA_200 TS047_RoL_RNA_204 TS047_RoL_RNA_229 TS047_RoL_RNA_231 TS047_RoL_RNA_258 TS047_RoL_RNA_262 TS047_RoL_RNA_286 TS047_RoL_RNA_288 TS047_RoL_RNA_289 TS047_RoL_RNA_291 TS047_RoL_RNA_317 TS047_RoL_RNA_318 TS047_RoL_RNA_319 TS047_RoL_RNA_322 TS047_RoL_RNA_326 TS047_RoL_RNA_328 TS047_RoL_RNA_347 TS047_RoL_RNA_355 TS047_RoL_RNA_377 TS047_RoL_RNA_381 TS047_RoL_RNA_407 TS047_RoL_RNA_412 TS047_RoL_RNA_439 TS047_RoL_RNA_442 TS047_RoL_RNA_46 TS047_RoL_RNA_468 TS047_RoL_RNA_469 TS047_RoL_RNA_477 TS047_RoL_RNA_478 TS047_RoL_RNA_498 TS047_RoL_RNA_500 TS047_RoL_RNA_502 TS047_RoL_RNA_506 TS047_RoL_RNA_51 TS047_RoL_RNA_526 TS047_RoL_RNA_528 TS047_RoL_RNA_530 TS047_RoL_RNA_532 TS047_RoL_RNA_559 TS047_RoL_RNA_561 TS047_RoL_RNA_562 TS047_RoL_RNA_586 TS047_RoL_RNA_616 TS047_RoL_RNA_618 TS047_RoL_RNA_646 TS047_RoL_RNA_651 TS047_RoL_RNA_652 TS047_RoL_RNA_655 TS047_RoL_RNA_676 TS047_RoL_RNA_677 TS047_RoL_RNA_678 TS047_RoL_RNA_679 TS047_RoL_RNA_683 TS047_RoL_RNA_707 TS047_RoL_RNA_708 TS047_RoL_RNA_710 TS047_RoL_RNA_79 TS047_RoL_RNA_85
cat("Available assays:", assayNames(se), "\n")
## Available assays: counts abundance
cat("Column data (metadata):", names(colData(se)), "\n")
## Column data (metadata): sample fastq_1 fastq_2 strandedness
# Clean sample names by removing "TS047_RoL_RNA_" prefix
clean_names <- gsub("TS047_RoL_RNA_", "", colnames(se))
# Update column names in the SummarizedExperiment object
colnames(se) <- clean_names
# Correct specific sample names if needed
# Rename sample 136 to 138
clean_names[clean_names == "136"] <- "138"
colnames(se) <- clean_names
# Create a data frame for the metadata columns we want to add
metadata_cols <- c("Time", "Antibiotics", "Temperature",
"Pathogen", "History", "Length.mm", "Weight.g", "Total.Worm.Count")
# Initialize a data frame to store the metadata
sample_metadata <- data.frame(
Sample_Name = clean_names,
stringsAsFactors = FALSE
)
rownames(sample_metadata) <- clean_names
# Add each metadata column
for (col in metadata_cols) {
values <- rep(NA, length(clean_names))
for (i in seq_along(clean_names)) {
matches <- which(Metadata$Sample_Name == clean_names[i])
if (length(matches) == 1) {
values[i] <- Metadata[matches, col, drop = TRUE]
}
}
sample_metadata[[col]] <- values
}
# Add the metadata to the SummarizedExperiment object
colData(se) <- DataFrame(sample_metadata)
cat("Metadata added to SummarizedExperiment object\n")
## Metadata added to SummarizedExperiment object
# Remove samples with NA values in treatment columns
se_filtered <- se[, !is.na(colData(se)$Antibiotics) & !is.na(colData(se)$Temperature) & !is.na(colData(se)$Pathogen)]
cat("Number of samples after removing NAs:", ncol(se_filtered), "\n")
## Number of samples after removing NAs: 71
# Create treatment combinations using DESeq2-compatible format
colData(se_filtered)$Treatment <- paste0(
ifelse(colData(se_filtered)$Antibiotics == 1, "A_plus", "A_minus"), "_",
ifelse(colData(se_filtered)$Temperature == 1, "T_plus", "T_minus"), "_",
ifelse(colData(se_filtered)$Pathogen == 1, "P_plus", "P_minus")
)
# Create plotting-friendly treatment names
colData(se_filtered)$Treatment_Plot <- paste0(
ifelse(colData(se_filtered)$Antibiotics == 1, "A+", "A-"), " ",
ifelse(colData(se_filtered)$Temperature == 1, "T+", "T-"), " ",
ifelse(colData(se_filtered)$Pathogen == 1, "P+", "P-")
)
# Convert treatment to factor with specified order (DESeq2 names)
colData(se_filtered)$Treatment <- factor(colData(se_filtered)$Treatment, levels = treatment_order_deseq)
# Convert plotting treatment to factor with specified order
colData(se_filtered)$Treatment_Plot <- factor(colData(se_filtered)$Treatment_Plot, levels = treatment_order_plot)
# Print the distribution of treatment combinations
cat("\nTreatment combination distribution:\n")
##
## Treatment combination distribution:
print(table(colData(se_filtered)$Treatment))
##
## A_minus_T_minus_P_minus A_minus_T_minus_P_plus A_plus_T_minus_P_minus
## 6 11 6
## A_plus_T_minus_P_plus A_minus_T_plus_P_minus A_minus_T_plus_P_plus
## 12 6 12
## A_plus_T_plus_P_minus A_plus_T_plus_P_plus
## 6 12
print(table(colData(se_filtered)$Treatment_Plot))
##
## A- T- P- A- T- P+ A+ T- P- A+ T- P+ A- T+ P- A- T+ P+ A+ T+ P- A+ T+ P+
## 6 11 6 12 6 12 6 12
# Clean other factor levels
colData(se_filtered)$Time <- factor(colData(se_filtered)$Time)
colData(se_filtered)$Antibiotics <- factor(colData(se_filtered)$Antibiotics)
colData(se_filtered)$Temperature <- factor(colData(se_filtered)$Temperature)
colData(se_filtered)$Pathogen <- factor(colData(se_filtered)$Pathogen)
# Create initial design formula
design_formula <- ~ Treatment
# Use length-scaled counts for DESeq2 analysis
if (!"counts" %in% assayNames(se_filtered)) {
# Read in the length-scaled counts file
length_scaled_counts <- read.table(here::here("Data", "Transcriptomics", "Results", "rnaseq", "051525", "salmon", "salmon.merged.gene_counts_length_scaled.tsv"),
header = TRUE, row.names = 1)
# Convert to matrix and ensure it's numeric
counts_matrix <- as.matrix(length_scaled_counts)
mode(counts_matrix) <- "numeric"
# Round to nearest integer (DESeq2 requires integer counts)
counts_matrix <- round(counts_matrix)
# Ensure the order of samples matches the SummarizedExperiment
counts_matrix <- counts_matrix[, colnames(se_filtered)]
} else {
# If counts are available, use them
counts_matrix <- as.matrix(assays(se_filtered)$counts)
mode(counts_matrix) <- "numeric"
counts_matrix <- round(counts_matrix)
}
# Create initial DESeq2 dataset
dds_initial <- DESeqDataSetFromMatrix(
countData = counts_matrix,
colData = colData(se_filtered),
design = design_formula
)
## converting counts to integer mode
# Pre-filtering: remove low abundance transcripts
cpm <- counts(dds_initial) / colSums(counts(dds_initial)) * 1e6
# Keep genes that have at least 2 CPM in at least 3 samples
keep <- rowSums(cpm >= 2) >= 3
dds_filtered <- dds_initial[keep,]
# Print filtering statistics
cat("Number of genes before filtering:", nrow(counts_matrix), "\n")
## Number of genes before filtering: 39447
cat("Number of genes after filtering:", nrow(dds_filtered), "\n")
## Number of genes after filtering: 20664
cat("Number of genes removed:", nrow(counts_matrix) - nrow(dds_filtered), "\n")
## Number of genes removed: 18783
cat("Percentage of genes kept:", round(nrow(dds_filtered)/nrow(counts_matrix)*100, 2), "%\n")
## Percentage of genes kept: 52.38 %
# Transform counts for visualization
rld <- vst(dds_filtered, blind=FALSE)
# Estimate size factors
dds_filtered <- estimateSizeFactors(dds_filtered)
# Get normalized counts
normalized_counts <- counts(dds_filtered, normalized=TRUE)
# After dds_filtered is created and before any downstream analyses:
# List of genes to exclude
genes_to_exclude <- c(
"zgc:112970",
"lectin",
"zp2.6",
"qdprb.4",
"bncr",
"avd",
"tdgf1",
"adad2",
"LOC137488852",
"ppt2a.1",
"snapc1a",
"exd1",
"LOC141381090",
"LOC141381093",
"LOC141378343",
"LOC101884348"
)
# Remove these genes from dds_filtered, rld, and normalized_counts
keep_genes <- !(rownames(dds_filtered) %in% genes_to_exclude)
dds_filtered <- dds_filtered[keep_genes, ]
# Re-transform counts for visualization after filtering
rld <- vst(dds_filtered, blind=FALSE)
# Estimate size factors again after filtering
dds_filtered <- estimateSizeFactors(dds_filtered)
# Get normalized counts after filtering
normalized_counts <- counts(dds_filtered, normalized=TRUE)
# Print exclusion summary
cat("Number of genes excluded:", length(genes_to_exclude), "\n")
## Number of genes excluded: 16
cat("Number of genes remaining after exclusion:", nrow(dds_filtered), "\n")
## Number of genes remaining after exclusion: 20648
# Enhanced parallel processing setup
# Detect number of available cores
available_cores <- parallel::detectCores()
cat("Available cores:", available_cores, "\n")
## Available cores: 10
# Use 75% of available cores to avoid overwhelming the system
# Leave some cores free for other processes
num_cores <- max(1, floor(available_cores * 0.75))
cat("Using cores for parallel processing:", num_cores, "\n")
## Using cores for parallel processing: 7
# Create optimized BiocParallel parameters
bp_param <- MulticoreParam(
workers = num_cores,
tasks = num_cores * 2, # Increase task granularity
progressbar = TRUE # Enable progress reporting
)
# Register the optimized parameters
register(bp_param)
cat("Parallel processing configured with", num_cores, "cores\n")
## Parallel processing configured with 7 cores
cat("Task granularity:", bp_param$tasks, "\n")
## Task granularity: 14
cat("Progress bar enabled:", bp_param$progressbar, "\n")
## Progress bar enabled: TRUE
# Define the specific comparisons for our analysis
comparisons <- list(
# 1. All Treatment Groups (comprehensive analysis)
"All_Treatments" = list(
description = "Comprehensive analysis across all treatment combinations",
design = ~ Treatment,
contrasts = list(
"A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_minus_T_minus_P_plus", "A_minus_T_minus_P_minus"),
"A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_plus_T_minus_P_minus", "A_minus_T_minus_P_minus"),
"A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_plus_T_minus_P_plus", "A_minus_T_minus_P_minus"),
"A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_minus_T_plus_P_minus", "A_minus_T_minus_P_minus"),
"A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_minus_T_plus_P_plus", "A_minus_T_minus_P_minus"),
"A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_plus_T_plus_P_minus", "A_minus_T_minus_P_minus"),
"A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_plus_T_plus_P_plus", "A_minus_T_minus_P_minus")
)
),
# 2. Parasite Effect (A_minus_T_minus_P_minus vs A_minus_T_minus_P_plus)
"Parasite_Effect" = list(
description = "Baseline parasite effect: A_minus_T_minus_P_minus vs A_minus_T_minus_P_plus",
design = ~ Treatment,
contrasts = list(
"A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_minus_T_minus_P_plus", "A_minus_T_minus_P_minus")
)
),
# 3. Historical Contingency (A_minus_T_minus_P_plus vs A_plus_T_minus_P_plus, A_minus_T_plus_P_plus, A_plus_T_plus_P_plus)
"Historical_Contingency" = list(
description = "How prior stressors affect parasite response: A_minus_T_minus_P_plus vs (A_plus_T_minus_P_plus, A_minus_T_plus_P_plus, A_plus_T_plus_P_plus)",
design = ~ Treatment,
contrasts = list(
"A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_plus" = c("Treatment", "A_plus_T_minus_P_plus", "A_minus_T_minus_P_plus"),
"A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_plus" = c("Treatment", "A_minus_T_plus_P_plus", "A_minus_T_minus_P_plus"),
"A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_plus" = c("Treatment", "A_plus_T_plus_P_plus", "A_minus_T_minus_P_plus")
)
),
# 4. Recovery Analysis (A_minus_T_minus_P_minus vs A_plus_T_minus_P_minus, A_minus_T_plus_P_minus, A_plus_T_plus_P_minus)
"Recovery_Analysis" = list(
description = "How prior stressors affect recovery: A_minus_T_minus_P_minus vs (A_plus_T_minus_P_minus, A_minus_T_plus_P_minus, A_plus_T_plus_P_minus)",
design = ~ Treatment,
contrasts = list(
"A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_plus_T_minus_P_minus", "A_minus_T_minus_P_minus"),
"A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_minus_T_plus_P_minus", "A_minus_T_minus_P_minus"),
"A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_plus_T_plus_P_minus", "A_minus_T_minus_P_minus")
)
)
)
## using ntop=500 top features by variance
# Check which analyses have saved results
cat("=== Checking for saved results ===\n")
## === Checking for saved results ===
for (analysis_name in names(comparisons)) {
if (results_exist(analysis_name)) {
cat("✓", analysis_name, "- results found\n")
} else {
cat("✗", analysis_name, "- no saved results\n")
}
}
## ✓ All_Treatments - results found
## ✓ Parasite_Effect - results found
## ✓ Historical_Contingency - results found
## ✓ Recovery_Analysis - results found
# Set this to TRUE if you want to recompute all analyses
# Set to FALSE to use existing results when available
force_recompute_all <- FALSE
# You can also set individual analyses to recompute
force_recompute_individual <- list(
"All_Treatments" = FALSE,
"Parasite_Effect" = FALSE,
"Historical_Contingency" = FALSE,
"Recovery_Analysis" = FALSE
)
cat("\nForce recompute all:", force_recompute_all, "\n")
##
## Force recompute all: FALSE
cat("Individual force recompute settings:\n")
## Individual force recompute settings:
for (analysis_name in names(force_recompute_individual)) {
cat(" ", analysis_name, ":", force_recompute_individual[[analysis_name]], "\n")
}
## All_Treatments : FALSE
## Parasite_Effect : FALSE
## Historical_Contingency : FALSE
## Recovery_Analysis : FALSE
# Uncomment the lines below if you want to clean up saved results
# cleanup_saved_results() # Remove all saved results
# cleanup_saved_results(c("All_Treatments", "Parasite_Effect")) # Remove specific analyses
cat("\n=== Usage Instructions ===\n")
##
## === Usage Instructions ===
cat("1. Set force_recompute_all = TRUE to recompute all analyses\n")
## 1. Set force_recompute_all = TRUE to recompute all analyses
cat("2. Set individual force_recompute_individual values to TRUE to recompute specific analyses\n")
## 2. Set individual force_recompute_individual values to TRUE to recompute specific analyses
cat("3. Use cleanup_saved_results() to remove all saved results\n")
## 3. Use cleanup_saved_results() to remove all saved results
cat("4. Use cleanup_saved_results(c('analysis1', 'analysis2')) to remove specific analyses\n")
## 4. Use cleanup_saved_results(c('analysis1', 'analysis2')) to remove specific analyses
# Monitor initial performance
cat("=== Starting DESeq2 Analysis ===\n")
## === Starting DESeq2 Analysis ===
monitor_performance()
## === Performance Monitor ===
## Memory usage:
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8802039 470.1 16282930 869.7 NA 16282930 869.7
## Vcells 32613476 248.9 57073799 435.5 32768 47494646 362.4
## CPU info:
## CPU usage: 18.44% user, 22.63% sys, 58.91% idle
## Active parallel workers: 7
## ========================
# Optimize memory before starting
optimize_memory()
## Optimizing memory usage...
## Memory optimization complete
# Run all analyses
all_results <- list()
for (analysis_name in names(comparisons)) {
cat("\n--- Starting analysis:", analysis_name, "---\n")
# Monitor performance before each analysis
monitor_performance()
# Run the analysis
all_results[[analysis_name]] <- run_analysis_set(analysis_name, comparisons[[analysis_name]], force_recompute_all || force_recompute_individual[[analysis_name]])
# Optimize memory after each analysis
optimize_memory()
cat("--- Completed analysis:", analysis_name, "---\n")
}
##
## --- Starting analysis: All_Treatments ---
## === Performance Monitor ===
## Memory usage:
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8802192 470.1 16282930 869.7 NA 16282930 869.7
## Vcells 32614304 248.9 57073799 435.5 32768 47494646 362.4
## CPU info:
## CPU usage: 11.85% user, 11.73% sys, 76.41% idle
## Active parallel workers: 7
## ========================
##
## === Running All_Treatments ===
## Description: Comprehensive analysis across all treatment combinations
## Loading existing results for All_Treatments
## Loading existing results for: All_Treatments
## Optimizing memory usage...
## Memory optimization complete
## --- Completed analysis: All_Treatments ---
##
## --- Starting analysis: Parasite_Effect ---
## === Performance Monitor ===
## Memory usage:
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8803051 470.2 16282930 869.7 NA 16282930 869.7
## Vcells 33630989 256.6 57073799 435.5 32768 47494646 362.4
## CPU info:
## CPU usage: 18.91% user, 13.93% sys, 67.14% idle
## Active parallel workers: 7
## ========================
##
## === Running Parasite_Effect ===
## Description: Baseline parasite effect: A_minus_T_minus_P_minus vs A_minus_T_minus_P_plus
## Loading existing results for Parasite_Effect
## Loading existing results for: Parasite_Effect
## Optimizing memory usage...
## Memory optimization complete
## --- Completed analysis: Parasite_Effect ---
##
## --- Starting analysis: Historical_Contingency ---
## === Performance Monitor ===
## Memory usage:
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8803190 470.2 16282930 869.7 NA 16282930 869.7
## Vcells 33776293 257.7 57073799 435.5 32768 47494646 362.4
## CPU info:
## CPU usage: 10.76% user, 11.12% sys, 78.10% idle
## Active parallel workers: 7
## ========================
##
## === Running Historical_Contingency ===
## Description: How prior stressors affect parasite response: A_minus_T_minus_P_plus vs (A_plus_T_minus_P_plus, A_minus_T_plus_P_plus, A_plus_T_plus_P_plus)
## Loading existing results for Historical_Contingency
## Loading existing results for: Historical_Contingency
## Optimizing memory usage...
## Memory optimization complete
## --- Completed analysis: Historical_Contingency ---
##
## --- Starting analysis: Recovery_Analysis ---
## === Performance Monitor ===
## Memory usage:
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8803415 470.2 16282930 869.7 NA 16282930 869.7
## Vcells 34211196 261.1 57073799 435.5 32768 47494646 362.4
## CPU info:
## CPU usage: 12.82% user, 13.69% sys, 73.48% idle
## Active parallel workers: 7
## ========================
##
## === Running Recovery_Analysis ===
## Description: How prior stressors affect recovery: A_minus_T_minus_P_minus vs (A_plus_T_minus_P_minus, A_minus_T_plus_P_minus, A_plus_T_plus_P_minus)
## Loading existing results for Recovery_Analysis
## Loading existing results for: Recovery_Analysis
## Optimizing memory usage...
## Memory optimization complete
## --- Completed analysis: Recovery_Analysis ---
# Final performance check
cat("\n=== Final Performance Check ===\n")
##
## === Final Performance Check ===
monitor_performance()
## === Performance Monitor ===
## Memory usage:
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8803577 470.2 16282930 869.7 NA 16282930 869.7
## Vcells 34645555 264.4 57073799 435.5 32768 47494646 362.4
## CPU info:
## CPU usage: 12.24% user, 12.36% sys, 75.39% idle
## Active parallel workers: 7
## ========================
# Print summary of results
cat("\n=== Analysis Summary ===\n")
##
## === Analysis Summary ===
for (analysis_name in names(all_results)) {
cat("\n", analysis_name, ":\n")
for (contrast_name in names(all_results[[analysis_name]])) {
res <- all_results[[analysis_name]][[contrast_name]]
cat(" ", contrast_name, ":\n")
cat(" Significant genes (padj < 0.05):", sum(res$padj < 0.05, na.rm=TRUE), "\n")
cat(" Upregulated genes:", sum(res$padj < 0.05 & res$log2FoldChange > 0, na.rm=TRUE), "\n")
cat(" Downregulated genes:", sum(res$padj < 0.05 & res$log2FoldChange < 0, na.rm=TRUE), "\n")
}
}
##
## All_Treatments :
## A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus :
## Significant genes (padj < 0.05): 3753
## Upregulated genes: 1994
## Downregulated genes: 1759
## A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus :
## Significant genes (padj < 0.05): 35
## Upregulated genes: 8
## Downregulated genes: 27
## A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_minus :
## Significant genes (padj < 0.05): 6473
## Upregulated genes: 3453
## Downregulated genes: 3020
## A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus :
## Significant genes (padj < 0.05): 47
## Upregulated genes: 6
## Downregulated genes: 41
## A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_minus :
## Significant genes (padj < 0.05): 6196
## Upregulated genes: 3235
## Downregulated genes: 2961
## A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus :
## Significant genes (padj < 0.05): 117
## Upregulated genes: 18
## Downregulated genes: 99
## A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_minus :
## Significant genes (padj < 0.05): 5017
## Upregulated genes: 2603
## Downregulated genes: 2414
##
## Parasite_Effect :
## A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus :
## Significant genes (padj < 0.05): 3753
## Upregulated genes: 1994
## Downregulated genes: 1759
##
## Historical_Contingency :
## A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_plus :
## Significant genes (padj < 0.05): 49
## Upregulated genes: 26
## Downregulated genes: 23
## A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_plus :
## Significant genes (padj < 0.05): 137
## Upregulated genes: 93
## Downregulated genes: 44
## A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_plus :
## Significant genes (padj < 0.05): 18
## Upregulated genes: 5
## Downregulated genes: 13
##
## Recovery_Analysis :
## A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus :
## Significant genes (padj < 0.05): 35
## Upregulated genes: 8
## Downregulated genes: 27
## A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus :
## Significant genes (padj < 0.05): 47
## Upregulated genes: 6
## Downregulated genes: 41
## A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus :
## Significant genes (padj < 0.05): 117
## Upregulated genes: 18
## Downregulated genes: 99
## Number of genes excluded: 16
## Number of genes remaining in top_genes_list: 95
summary_table
| Summary of Differential Gene Expression | ||||
| All Treatment Groups Analysis | ||||
| Treatment Comparison | Total Genes | Significant Genes | Upregulated | Downregulated |
|---|---|---|---|---|
| A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus | 20,648 | 3,753 | 1,994 | 1,759 |
| A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus | 20,648 | 35 | 8 | 27 |
| A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_minus | 20,648 | 6,473 | 3,453 | 3,020 |
| A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus | 20,648 | 47 | 6 | 41 |
| A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_minus | 20,648 | 6,196 | 3,235 | 2,961 |
| A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus | 20,648 | 117 | 18 | 99 |
| A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_minus | 20,648 | 5,017 | 2,603 | 2,414 |
## ### Top 10 Upregulated Genes: A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus
## ### Top 10 Downregulated Genes: A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus
## ### Top 10 Upregulated Genes: A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus
## ### Top 10 Downregulated Genes: A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus
## ### Top 10 Upregulated Genes: A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_minus
## ### Top 10 Downregulated Genes: A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_minus
## ### Top 10 Upregulated Genes: A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus
## ### Top 10 Downregulated Genes: A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus
## ### Top 10 Upregulated Genes: A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_minus
## ### Top 10 Downregulated Genes: A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_minus
## ### Top 10 Upregulated Genes: A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus
## ### Top 10 Downregulated Genes: A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus
## ### Top 10 Upregulated Genes: A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_minus
## ### Top 10 Downregulated Genes: A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_minus
summary_table
| Summary of Differential Gene Expression | ||||
| Parasite Effect Analysis (A- T- P- vs A- T- P+) | ||||
| Treatment Comparison | Total Genes | Significant Genes | Upregulated | Downregulated |
|---|---|---|---|---|
| A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus | 20,648 | 3,753 | 1,994 | 1,759 |
## ### Top 20 Significant Genes: A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus
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## <thead>
## <tr class="gt_heading">
## <td colspan="4" class="gt_heading gt_title gt_font_normal gt_bottom_border" style>Top 20 Significant Genes: Parasite Effect</td>
## </tr>
##
## <tr class="gt_col_headings">
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="Gene">Gene</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="log2 Fold Change">log2 Fold Change</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Adjusted p-value">Adjusted p-value</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Base Mean">Base Mean</th>
## </tr>
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## <tbody class="gt_table_body">
## <tr><td headers="gene" class="gt_row gt_left">gbp1</td>
## <td headers="log2FoldChange" class="gt_row gt_right">3.78</td>
## <td headers="padj" class="gt_row gt_right">2.550 × 10<sup style='font-size: 65%;'>−15</sup></td>
## <td headers="baseMean" class="gt_row gt_right">4,447.72</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">zgc:110540</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.92</td>
## <td headers="padj" class="gt_row gt_right">1.337 × 10<sup style='font-size: 65%;'>−13</sup></td>
## <td headers="baseMean" class="gt_row gt_right">174.69</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">ercc6l</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.70</td>
## <td headers="padj" class="gt_row gt_right">2.107 × 10<sup style='font-size: 65%;'>−13</sup></td>
## <td headers="baseMean" class="gt_row gt_right">250.82</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">tapbpl</td>
## <td headers="log2FoldChange" class="gt_row gt_right">1.97</td>
## <td headers="padj" class="gt_row gt_right">2.296 × 10<sup style='font-size: 65%;'>−13</sup></td>
## <td headers="baseMean" class="gt_row gt_right">718.48</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">batf2</td>
## <td headers="log2FoldChange" class="gt_row gt_right">4.57</td>
## <td headers="padj" class="gt_row gt_right">1.618 × 10<sup style='font-size: 65%;'>−12</sup></td>
## <td headers="baseMean" class="gt_row gt_right">462.49</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC101885672</td>
## <td headers="log2FoldChange" class="gt_row gt_right">4.69</td>
## <td headers="padj" class="gt_row gt_right">2.264 × 10<sup style='font-size: 65%;'>−12</sup></td>
## <td headers="baseMean" class="gt_row gt_right">1,001.46</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">gbp2</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.74</td>
## <td headers="padj" class="gt_row gt_right">3.086 × 10<sup style='font-size: 65%;'>−12</sup></td>
## <td headers="baseMean" class="gt_row gt_right">978.30</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">pcna</td>
## <td headers="log2FoldChange" class="gt_row gt_right">1.83</td>
## <td headers="padj" class="gt_row gt_right">3.971 × 10<sup style='font-size: 65%;'>−12</sup></td>
## <td headers="baseMean" class="gt_row gt_right">2,492.46</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">zgc:101715</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.32</td>
## <td headers="padj" class="gt_row gt_right">6.316 × 10<sup style='font-size: 65%;'>−12</sup></td>
## <td headers="baseMean" class="gt_row gt_right">456.29</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">anxa3b</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.20</td>
## <td headers="padj" class="gt_row gt_right">3.440 × 10<sup style='font-size: 65%;'>−11</sup></td>
## <td headers="baseMean" class="gt_row gt_right">3,058.49</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">irf10</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.64</td>
## <td headers="padj" class="gt_row gt_right">5.490 × 10<sup style='font-size: 65%;'>−11</sup></td>
## <td headers="baseMean" class="gt_row gt_right">568.74</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">dut</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.13</td>
## <td headers="padj" class="gt_row gt_right">5.818 × 10<sup style='font-size: 65%;'>−11</sup></td>
## <td headers="baseMean" class="gt_row gt_right">513.03</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">rab40b</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.10</td>
## <td headers="padj" class="gt_row gt_right">1.622 × 10<sup style='font-size: 65%;'>−10</sup></td>
## <td headers="baseMean" class="gt_row gt_right">383.74</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">rfc4</td>
## <td headers="log2FoldChange" class="gt_row gt_right">1.60</td>
## <td headers="padj" class="gt_row gt_right">2.551 × 10<sup style='font-size: 65%;'>−10</sup></td>
## <td headers="baseMean" class="gt_row gt_right">296.30</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">ncapd3</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.49</td>
## <td headers="padj" class="gt_row gt_right">3.553 × 10<sup style='font-size: 65%;'>−10</sup></td>
## <td headers="baseMean" class="gt_row gt_right">225.60</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">smc2</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.16</td>
## <td headers="padj" class="gt_row gt_right">5.299 × 10<sup style='font-size: 65%;'>−10</sup></td>
## <td headers="baseMean" class="gt_row gt_right">410.25</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">zgc:194101</td>
## <td headers="log2FoldChange" class="gt_row gt_right">3.67</td>
## <td headers="padj" class="gt_row gt_right">9.834 × 10<sup style='font-size: 65%;'>−10</sup></td>
## <td headers="baseMean" class="gt_row gt_right">958.86</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">acp2</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−1.55</td>
## <td headers="padj" class="gt_row gt_right">1.194 × 10<sup style='font-size: 65%;'>−9</sup></td>
## <td headers="baseMean" class="gt_row gt_right">1,703.10</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">klhdc3</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−0.89</td>
## <td headers="padj" class="gt_row gt_right">1.194 × 10<sup style='font-size: 65%;'>−9</sup></td>
## <td headers="baseMean" class="gt_row gt_right">784.36</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">nup93</td>
## <td headers="log2FoldChange" class="gt_row gt_right">1.34</td>
## <td headers="padj" class="gt_row gt_right">1.242 × 10<sup style='font-size: 65%;'>−9</sup></td>
## <td headers="baseMean" class="gt_row gt_right">792.81</td></tr>
## </tbody>
##
##
## </table>
## </div>
summary_table
| Historical Contingency Summary | |||
| Effect of prior stressors on parasite response | |||
| Treatment Comparison | Upregulated Genes | Downregulated Genes | Total Significant |
|---|---|---|---|
| ABX+PARA+ vs PARA+ | 26 | 23 | 49 |
| TEMP+PARA+ vs PARA+ | 93 | 44 | 137 |
| ABX+TEMP+PARA+ vs PARA+ | 5 | 13 | 18 |
## ### Top 15 Significant Genes: A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_plus
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## <thead>
## <tr class="gt_heading">
## <td colspan="4" class="gt_heading gt_title gt_font_normal gt_bottom_border" style>Top 15 Significant Genes: A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_plus</td>
## </tr>
##
## <tr class="gt_col_headings">
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="Gene">Gene</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="log2 Fold Change">log2 Fold Change</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Adjusted p-value">Adjusted p-value</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Base Mean">Base Mean</th>
## </tr>
## </thead>
## <tbody class="gt_table_body">
## <tr><td headers="gene" class="gt_row gt_left">LOC137490512</td>
## <td headers="log2FoldChange" class="gt_row gt_right">47.23</td>
## <td headers="padj" class="gt_row gt_right">2.104 × 10<sup style='font-size: 65%;'>−43</sup></td>
## <td headers="baseMean" class="gt_row gt_right">11.77</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC141382111</td>
## <td headers="log2FoldChange" class="gt_row gt_right">34.16</td>
## <td headers="padj" class="gt_row gt_right">1.267 × 10<sup style='font-size: 65%;'>−14</sup></td>
## <td headers="baseMean" class="gt_row gt_right">7.24</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC141374967</td>
## <td headers="log2FoldChange" class="gt_row gt_right">39.53</td>
## <td headers="padj" class="gt_row gt_right">7.357 × 10<sup style='font-size: 65%;'>−11</sup></td>
## <td headers="baseMean" class="gt_row gt_right">4.45</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">pvalb9</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−5.00</td>
## <td headers="padj" class="gt_row gt_right">4.066 × 10<sup style='font-size: 65%;'>−6</sup></td>
## <td headers="baseMean" class="gt_row gt_right">952.63</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">zgc:153738</td>
## <td headers="log2FoldChange" class="gt_row gt_right">3.66</td>
## <td headers="padj" class="gt_row gt_right">1.160 × 10<sup style='font-size: 65%;'>−5</sup></td>
## <td headers="baseMean" class="gt_row gt_right">38.40</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">zmp:0000000629</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−4.77</td>
## <td headers="padj" class="gt_row gt_right">9.427 × 10<sup style='font-size: 65%;'>−5</sup></td>
## <td headers="baseMean" class="gt_row gt_right">89.03</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC137487415</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.23</td>
## <td headers="padj" class="gt_row gt_right">2.823 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">37.99</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">crp7</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−3.69</td>
## <td headers="padj" class="gt_row gt_right">9.502 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">91.28</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">itga2b</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.53</td>
## <td headers="padj" class="gt_row gt_right">1.329 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">30.44</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">ugt5a4</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.35</td>
## <td headers="padj" class="gt_row gt_right">1.508 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">696.32</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC137487483</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−1.74</td>
## <td headers="padj" class="gt_row gt_right">1.816 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">369.03</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">cspp1a</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.83</td>
## <td headers="padj" class="gt_row gt_right">2.256 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">23.22</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">foxj1b</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−3.25</td>
## <td headers="padj" class="gt_row gt_right">2.487 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">5.77</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">gatm</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.03</td>
## <td headers="padj" class="gt_row gt_right">2.487 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">1,251.50</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">hydin</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−1.91</td>
## <td headers="padj" class="gt_row gt_right">2.487 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">60.02</td></tr>
## </tbody>
##
##
## </table>
## </div>
##
## ### Top 15 Significant Genes: A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_plus
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## <thead>
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## <td colspan="4" class="gt_heading gt_title gt_font_normal gt_bottom_border" style>Top 15 Significant Genes: A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_plus</td>
## </tr>
##
## <tr class="gt_col_headings">
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="Gene">Gene</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="log2 Fold Change">log2 Fold Change</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Adjusted p-value">Adjusted p-value</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Base Mean">Base Mean</th>
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## </thead>
## <tbody class="gt_table_body">
## <tr><td headers="gene" class="gt_row gt_left">LOC137490512</td>
## <td headers="log2FoldChange" class="gt_row gt_right">46.49</td>
## <td headers="padj" class="gt_row gt_right">5.864 × 10<sup style='font-size: 65%;'>−42</sup></td>
## <td headers="baseMean" class="gt_row gt_right">11.77</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC141382111</td>
## <td headers="log2FoldChange" class="gt_row gt_right">37.01</td>
## <td headers="padj" class="gt_row gt_right">1.105 × 10<sup style='font-size: 65%;'>−17</sup></td>
## <td headers="baseMean" class="gt_row gt_right">7.24</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC141374967</td>
## <td headers="log2FoldChange" class="gt_row gt_right">39.54</td>
## <td headers="padj" class="gt_row gt_right">7.311 × 10<sup style='font-size: 65%;'>−11</sup></td>
## <td headers="baseMean" class="gt_row gt_right">4.45</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC141375690</td>
## <td headers="log2FoldChange" class="gt_row gt_right">30.75</td>
## <td headers="padj" class="gt_row gt_right">9.231 × 10<sup style='font-size: 65%;'>−6</sup></td>
## <td headers="baseMean" class="gt_row gt_right">10.73</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">lsm7</td>
## <td headers="log2FoldChange" class="gt_row gt_right">0.74</td>
## <td headers="padj" class="gt_row gt_right">7.724 × 10<sup style='font-size: 65%;'>−5</sup></td>
## <td headers="baseMean" class="gt_row gt_right">576.60</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC137487415</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.51</td>
## <td headers="padj" class="gt_row gt_right">1.219 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">37.99</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">slc26a3.1</td>
## <td headers="log2FoldChange" class="gt_row gt_right">3.84</td>
## <td headers="padj" class="gt_row gt_right">1.219 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">186.97</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">hmgb2a</td>
## <td headers="log2FoldChange" class="gt_row gt_right">0.71</td>
## <td headers="padj" class="gt_row gt_right">4.169 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">3,270.81</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">lsm8</td>
## <td headers="log2FoldChange" class="gt_row gt_right">0.70</td>
## <td headers="padj" class="gt_row gt_right">4.169 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">255.36</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">si:ch211-194e1.7</td>
## <td headers="log2FoldChange" class="gt_row gt_right">23.03</td>
## <td headers="padj" class="gt_row gt_right">9.092 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">13.99</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">cirbpa</td>
## <td headers="log2FoldChange" class="gt_row gt_right">0.65</td>
## <td headers="padj" class="gt_row gt_right">1.528 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">6,839.51</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">dut</td>
## <td headers="log2FoldChange" class="gt_row gt_right">1.10</td>
## <td headers="padj" class="gt_row gt_right">1.528 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">513.03</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">patj</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−0.58</td>
## <td headers="padj" class="gt_row gt_right">1.528 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">894.79</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">vrk1</td>
## <td headers="log2FoldChange" class="gt_row gt_right">0.80</td>
## <td headers="padj" class="gt_row gt_right">1.528 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">386.41</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">nedd4l</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−0.64</td>
## <td headers="padj" class="gt_row gt_right">1.630 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">1,081.30</td></tr>
## </tbody>
##
##
## </table>
## </div>
##
## ### Top 15 Significant Genes: A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_plus
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## <td colspan="4" class="gt_heading gt_title gt_font_normal gt_bottom_border" style>Top 15 Significant Genes: A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_plus</td>
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##
## <tr class="gt_col_headings">
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="Gene">Gene</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="log2 Fold Change">log2 Fold Change</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Adjusted p-value">Adjusted p-value</th>
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## <tr><td headers="gene" class="gt_row gt_left">LOC137490512</td>
## <td headers="log2FoldChange" class="gt_row gt_right">47.03</td>
## <td headers="padj" class="gt_row gt_right">5.365 × 10<sup style='font-size: 65%;'>−43</sup></td>
## <td headers="baseMean" class="gt_row gt_right">11.77</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC141381096</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−41.69</td>
## <td headers="padj" class="gt_row gt_right">6.426 × 10<sup style='font-size: 65%;'>−26</sup></td>
## <td headers="baseMean" class="gt_row gt_right">19.89</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC141375690</td>
## <td headers="log2FoldChange" class="gt_row gt_right">30.39</td>
## <td headers="padj" class="gt_row gt_right">1.902 × 10<sup style='font-size: 65%;'>−5</sup></td>
## <td headers="baseMean" class="gt_row gt_right">10.73</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">zmp:0000000629</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−5.02</td>
## <td headers="padj" class="gt_row gt_right">2.690 × 10<sup style='font-size: 65%;'>−5</sup></td>
## <td headers="baseMean" class="gt_row gt_right">89.03</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">pvalb9</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−4.02</td>
## <td headers="padj" class="gt_row gt_right">2.994 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">952.63</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">si:ch211-194e1.7</td>
## <td headers="log2FoldChange" class="gt_row gt_right">22.43</td>
## <td headers="padj" class="gt_row gt_right">2.994 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">13.99</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">celsr1b</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−3.14</td>
## <td headers="padj" class="gt_row gt_right">6.729 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">41.85</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">zp3d.1</td>
## <td headers="log2FoldChange" class="gt_row gt_right">3.22</td>
## <td headers="padj" class="gt_row gt_right">9.539 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">28.16</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">hydin</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.02</td>
## <td headers="padj" class="gt_row gt_right">1.368 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">60.02</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">igsf21b</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−3.99</td>
## <td headers="padj" class="gt_row gt_right">1.499 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">43.32</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">ifi27.6</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.46</td>
## <td headers="padj" class="gt_row gt_right">1.564 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">610.65</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC141379879</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−5.72</td>
## <td headers="padj" class="gt_row gt_right">1.564 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">99.05</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">ckmb</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−4.54</td>
## <td headers="padj" class="gt_row gt_right">1.970 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">52.80</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">slc4a5b</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−4.16</td>
## <td headers="padj" class="gt_row gt_right">3.315 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">342.17</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">abhd2a</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−0.92</td>
## <td headers="padj" class="gt_row gt_right">4.860 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">580.64</td></tr>
## </tbody>
##
##
## </table>
## </div>
summary_table
| Recovery Analysis Summary | |||
| Effect of prior stressors on recovery | |||
| Treatment Comparison | Upregulated Genes | Downregulated Genes | Total Significant |
|---|---|---|---|
| ABX+ vs Control | 8 | 27 | 35 |
| TEMP+ vs Control | 6 | 41 | 47 |
| ABX+TEMP+ vs Control | 18 | 99 | 117 |
## ### Top 15 Significant Genes: A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus
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## <td colspan="4" class="gt_heading gt_title gt_font_normal gt_bottom_border" style>Top 15 Significant Genes: A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus</td>
## </tr>
##
## <tr class="gt_col_headings">
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="Gene">Gene</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="log2 Fold Change">log2 Fold Change</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Adjusted p-value">Adjusted p-value</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Base Mean">Base Mean</th>
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## <tbody class="gt_table_body">
## <tr><td headers="gene" class="gt_row gt_left">LOC100147849</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−19.67</td>
## <td headers="padj" class="gt_row gt_right">8.847 × 10<sup style='font-size: 65%;'>−22</sup></td>
## <td headers="baseMean" class="gt_row gt_right">17.11</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">si:ch211-125e6.14</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−24.55</td>
## <td headers="padj" class="gt_row gt_right">3.610 × 10<sup style='font-size: 65%;'>−14</sup></td>
## <td headers="baseMean" class="gt_row gt_right">728.43</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">ncoa7a</td>
## <td headers="log2FoldChange" class="gt_row gt_right">3.39</td>
## <td headers="padj" class="gt_row gt_right">4.678 × 10<sup style='font-size: 65%;'>−6</sup></td>
## <td headers="baseMean" class="gt_row gt_right">672.56</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC103909395</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−16.57</td>
## <td headers="padj" class="gt_row gt_right">4.354 × 10<sup style='font-size: 65%;'>−5</sup></td>
## <td headers="baseMean" class="gt_row gt_right">6.21</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC110438438</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−9.78</td>
## <td headers="padj" class="gt_row gt_right">2.514 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">159.54</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC137491340</td>
## <td headers="log2FoldChange" class="gt_row gt_right">19.19</td>
## <td headers="padj" class="gt_row gt_right">4.002 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">12.62</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC101882847</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−6.61</td>
## <td headers="padj" class="gt_row gt_right">5.176 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">114.36</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC141379337</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−9.32</td>
## <td headers="padj" class="gt_row gt_right">1.265 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">69.70</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC141379345</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−9.97</td>
## <td headers="padj" class="gt_row gt_right">1.569 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">48.08</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC141379342</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−5.80</td>
## <td headers="padj" class="gt_row gt_right">2.578 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">40.33</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">pla2g3</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−4.77</td>
## <td headers="padj" class="gt_row gt_right">2.638 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">143.64</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">ccl35.1</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−3.47</td>
## <td headers="padj" class="gt_row gt_right">5.820 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">65.26</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">si:dkey-3k24.8</td>
## <td headers="log2FoldChange" class="gt_row gt_right">3.16</td>
## <td headers="padj" class="gt_row gt_right">6.386 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">112.79</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">ankrd66</td>
## <td headers="log2FoldChange" class="gt_row gt_right">18.08</td>
## <td headers="padj" class="gt_row gt_right">8.219 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">4.74</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC137487211</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.71</td>
## <td headers="padj" class="gt_row gt_right">1.279 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">36.37</td></tr>
## </tbody>
##
##
## </table>
## </div>
##
## ### Top 15 Significant Genes: A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus
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## <tr class="gt_heading">
## <td colspan="4" class="gt_heading gt_title gt_font_normal gt_bottom_border" style>Top 15 Significant Genes: A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus</td>
## </tr>
##
## <tr class="gt_col_headings">
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="Gene">Gene</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="log2 Fold Change">log2 Fold Change</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Adjusted p-value">Adjusted p-value</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Base Mean">Base Mean</th>
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## <tbody class="gt_table_body">
## <tr><td headers="gene" class="gt_row gt_left">LOC137487668</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−23.06</td>
## <td headers="padj" class="gt_row gt_right">1.472 × 10<sup style='font-size: 65%;'>−11</sup></td>
## <td headers="baseMean" class="gt_row gt_right">17.22</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">cpdb</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−18.35</td>
## <td headers="padj" class="gt_row gt_right">2.208 × 10<sup style='font-size: 65%;'>−9</sup></td>
## <td headers="baseMean" class="gt_row gt_right">10.44</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC141381605</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−23.61</td>
## <td headers="padj" class="gt_row gt_right">2.209 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">29.88</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">lhx8a</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−17.40</td>
## <td headers="padj" class="gt_row gt_right">5.190 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">5.45</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">nots</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−8.89</td>
## <td headers="padj" class="gt_row gt_right">5.190 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">4,683.87</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC137491340</td>
## <td headers="log2FoldChange" class="gt_row gt_right">18.83</td>
## <td headers="padj" class="gt_row gt_right">6.818 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">12.62</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">vtg5</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−8.78</td>
## <td headers="padj" class="gt_row gt_right">7.009 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">206,858.02</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">rcn3</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−4.67</td>
## <td headers="padj" class="gt_row gt_right">1.652 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">1,094.80</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">rtn1a</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−3.83</td>
## <td headers="padj" class="gt_row gt_right">2.503 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">2,599.05</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">mthfr</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.61</td>
## <td headers="padj" class="gt_row gt_right">3.492 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">364.46</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">mboat2a</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.08</td>
## <td headers="padj" class="gt_row gt_right">3.788 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">222.02</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">slc43a1a</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.34</td>
## <td headers="padj" class="gt_row gt_right">3.788 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">246.46</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">slc7a1b</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.05</td>
## <td headers="padj" class="gt_row gt_right">3.788 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">173.73</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">vtg7</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−9.38</td>
## <td headers="padj" class="gt_row gt_right">3.788 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">141,150.32</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">vtg8</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−6.25</td>
## <td headers="padj" class="gt_row gt_right">3.788 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">134.46</td></tr>
## </tbody>
##
##
## </table>
## </div>
##
## ### Top 15 Significant Genes: A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus
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## </style>
## <table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
## <thead>
## <tr class="gt_heading">
## <td colspan="4" class="gt_heading gt_title gt_font_normal gt_bottom_border" style>Top 15 Significant Genes: A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus</td>
## </tr>
##
## <tr class="gt_col_headings">
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="Gene">Gene</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="log2 Fold Change">log2 Fold Change</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Adjusted p-value">Adjusted p-value</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Base Mean">Base Mean</th>
## </tr>
## </thead>
## <tbody class="gt_table_body">
## <tr><td headers="gene" class="gt_row gt_left">LOC101885452</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−21.14</td>
## <td headers="padj" class="gt_row gt_right">1.759 × 10<sup style='font-size: 65%;'>−27</sup></td>
## <td headers="baseMean" class="gt_row gt_right">27.72</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC101887118</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−19.26</td>
## <td headers="padj" class="gt_row gt_right">1.655 × 10<sup style='font-size: 65%;'>−11</sup></td>
## <td headers="baseMean" class="gt_row gt_right">8.03</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">mhc2dgb</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−26.07</td>
## <td headers="padj" class="gt_row gt_right">4.051 × 10<sup style='font-size: 65%;'>−7</sup></td>
## <td headers="baseMean" class="gt_row gt_right">256.45</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC137495296</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−10.77</td>
## <td headers="padj" class="gt_row gt_right">8.250 × 10<sup style='font-size: 65%;'>−5</sup></td>
## <td headers="baseMean" class="gt_row gt_right">226.20</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC137491340</td>
## <td headers="log2FoldChange" class="gt_row gt_right">19.55</td>
## <td headers="padj" class="gt_row gt_right">2.767 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">12.62</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC101882702</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−4.80</td>
## <td headers="padj" class="gt_row gt_right">4.937 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">378.81</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">si:dkey-211g8.5</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−3.74</td>
## <td headers="padj" class="gt_row gt_right">5.647 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">198.63</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">ly6m5</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−4.64</td>
## <td headers="padj" class="gt_row gt_right">6.740 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">279.80</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">pld4</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−3.03</td>
## <td headers="padj" class="gt_row gt_right">1.180 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">132.58</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">stat1b</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.73</td>
## <td headers="padj" class="gt_row gt_right">1.293 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">2,635.38</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">ftr11</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.49</td>
## <td headers="padj" class="gt_row gt_right">1.620 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">142.87</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">LOC100001589</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.38</td>
## <td headers="padj" class="gt_row gt_right">1.620 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">553.61</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">mxa</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.66</td>
## <td headers="padj" class="gt_row gt_right">1.620 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">305.17</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">si:ch211-217k17.11</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.66</td>
## <td headers="padj" class="gt_row gt_right">1.620 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">6,447.32</td></tr>
## <tr><td headers="gene" class="gt_row gt_left">si:ch211-271e10.3</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.87</td>
## <td headers="padj" class="gt_row gt_right">1.620 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">2,015.31</td></tr>
## </tbody>
##
##
## </table>
## </div>
# Set up parallel processing for enrichment analysis
plan(multisession, workers = min(4, availableCores()))
# Run enrichment analysis for all three analyses
enrichment_results <- list()
for (analysis_name in names(all_results)) {
cat("\n=== Processing enrichment for:", analysis_name, "===\n")
# Check if we have results for this analysis
if (!is.null(all_results[[analysis_name]])) {
enrichment_results[[analysis_name]] <- run_enrichment_analysis(analysis_name, all_results[[analysis_name]])
} else {
cat("No results available for:", analysis_name, "\n")
}
}
##
## === Processing enrichment for: All_Treatments ===
##
## === Running Enrichment Analysis for: All_Treatments ===
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## Running GO enrichment...
## Performing GO enrichment for: A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus
## Number of genes: 1578
## 'select()' returned 1:1 mapping between keys and columns
## Performing GO enrichment for: A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus
## Number of genes: 23
## 'select()' returned 1:1 mapping between keys and columns
## Performing GO enrichment for: A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_minus
## Number of genes: 3076
## 'select()' returned 1:1 mapping between keys and columns
## Performing GO enrichment for: A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus
## Number of genes: 38
## 'select()' returned 1:1 mapping between keys and columns
## Performing GO enrichment for: A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_minus
## Number of genes: 2882
## 'select()' returned 1:1 mapping between keys and columns
## Performing GO enrichment for: A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus
## Number of genes: 89
## 'select()' returned 1:1 mapping between keys and columns
## Performing GO enrichment for: A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_minus
## Number of genes: 2242
## 'select()' returned 1:1 mapping between keys and columns
## Running KEGG enrichment...
## Performing KEGG enrichment for: A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus
## Number of genes: 1578
## Reading KEGG annotation online: "https://rest.kegg.jp/link/dre/pathway"...
## Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/dre"...
## Reading KEGG annotation online: "https://rest.kegg.jp/conv/ncbi-geneid/dre"...
## Performing KEGG enrichment for: A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus
## Number of genes: 23
## Performing KEGG enrichment for: A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_minus
## Number of genes: 3076
## Performing KEGG enrichment for: A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus
## Number of genes: 38
## Performing KEGG enrichment for: A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_minus
## Number of genes: 2882
## Performing KEGG enrichment for: A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus
## Number of genes: 89
## Performing KEGG enrichment for: A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_minus
## Number of genes: 2242
##
## === Processing enrichment for: Parasite_Effect ===
##
## === Running Enrichment Analysis for: Parasite_Effect ===
## 'select()' returned 1:many mapping between keys and columns
## Running GO enrichment...
## Performing GO enrichment for: A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus
## Number of genes: 1578
## 'select()' returned 1:1 mapping between keys and columns
## Running KEGG enrichment...
## Performing KEGG enrichment for: A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus
## Number of genes: 1578
##
## === Processing enrichment for: Historical_Contingency ===
##
## === Running Enrichment Analysis for: Historical_Contingency ===
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## Running GO enrichment...
## Performing GO enrichment for: A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_plus
## Number of genes: 36
## 'select()' returned 1:1 mapping between keys and columns
## Performing GO enrichment for: A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_plus
## Number of genes: 51
## 'select()' returned 1:1 mapping between keys and columns
## Performing GO enrichment for: A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_plus
## Number of genes: 13
## 'select()' returned 1:1 mapping between keys and columns
## Running KEGG enrichment...
## Performing KEGG enrichment for: A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_plus
## Number of genes: 36
## Performing KEGG enrichment for: A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_plus
## Number of genes: 51
## Performing KEGG enrichment for: A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_plus
## Number of genes: 13
##
## === Processing enrichment for: Recovery_Analysis ===
##
## === Running Enrichment Analysis for: Recovery_Analysis ===
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## Running GO enrichment...
## Performing GO enrichment for: A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus
## Number of genes: 23
## 'select()' returned 1:1 mapping between keys and columns
## Performing GO enrichment for: A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus
## Number of genes: 38
## 'select()' returned 1:1 mapping between keys and columns
## Performing GO enrichment for: A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus
## Number of genes: 89
## 'select()' returned 1:1 mapping between keys and columns
## Running KEGG enrichment...
## Performing KEGG enrichment for: A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus
## Number of genes: 23
## Performing KEGG enrichment for: A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus
## Number of genes: 38
## Performing KEGG enrichment for: A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus
## Number of genes: 89
# Clean up parallel processing
plan(sequential)
cat("\n=== Enrichment Analysis Complete ===\n")
##
## === Enrichment Analysis Complete ===
##
## === Processing All_Treatments ===
##
## === Processing Parasite_Effect ===
##
## === Processing Historical_Contingency ===
##
## === Processing Recovery_Analysis ===
##
## ## All_Treatments Enrichment Summary
##
## ### Top GO Terms
##
## ### Top KEGG Pathways
##
## ---
##
## ## Parasite_Effect Enrichment Summary
##
## ### Top GO Terms
##
## ### Top KEGG Pathways
##
## ---
##
## ## Historical_Contingency Enrichment Summary
##
## ### Top GO Terms
##
## ### Top KEGG Pathways
##
## ---
##
## ## Recovery_Analysis Enrichment Summary
##
## ### Top GO Terms
##
## ### Top KEGG Pathways
##
## ---
##
## ## Combined Summary Across All Analyses
##
## ### Combined GO Terms Summary
##
## ### Combined KEGG Pathways Summary
## $All_Treatments_GO
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##
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## <thead>
## <tr class="gt_heading">
## <td colspan="5" class="gt_heading gt_title gt_font_normal" style>Top GO Terms - All_Treatments</td>
## </tr>
## <tr class="gt_heading">
## <td colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style>Biological Process enrichment (top 10 per contrast)</td>
## </tr>
## <tr class="gt_col_headings">
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Treatment Comparison">Treatment Comparison</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="GO Term">GO Term</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="-log10(adj p-value)">-log10(adj p-value)</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Gene Count">Gene Count</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Mean log2FC">Mean log2FC</th>
## </tr>
## </thead>
## <tbody class="gt_table_body">
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">43.746</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">82</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.963</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">mitotic cell cycle process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">35.875</td>
## <td headers="Count" class="gt_row gt_right gt_striped">114</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.204</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA-templated DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">33.442</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">56</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.020</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">chromosome organization</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">31.704</td>
## <td headers="Count" class="gt_row gt_right gt_striped">94</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.083</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">31.165</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">79</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.272</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear division</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">28.063</td>
## <td headers="Count" class="gt_row gt_right gt_striped">72</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.269</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">27.219</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">104</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.964</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA damage response</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">27.194</td>
## <td headers="Count" class="gt_row gt_right gt_striped">122</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.901</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">nuclear chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.738</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">56</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.292</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organelle fission</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">25.633</td>
## <td headers="Count" class="gt_row gt_right gt_striped">74</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.219</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">8.202</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">13</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.390</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to virus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">8.202</td>
## <td headers="Count" class="gt_row gt_right gt_striped">8</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.820</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response to other organism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.622</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">11</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.700</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to biotic stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.622</td>
## <td headers="Count" class="gt_row gt_right gt_striped">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.653</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to external biotic stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.622</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.653</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to other organism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.622</td>
## <td headers="Count" class="gt_row gt_right gt_striped">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.653</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response to symbiont</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.901</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.735</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">defense response to virus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.901</td>
## <td headers="Count" class="gt_row gt_right gt_striped">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.735</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cytokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.734</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.223</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cellular response to cytokine stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.700</td>
## <td headers="Count" class="gt_row gt_right gt_striped">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.223</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">36.497</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">85</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.148</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">32.107</td>
## <td headers="Count" class="gt_row gt_right gt_striped">92</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.423</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">31.115</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">129</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.005</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA-templated DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">31.074</td>
## <td headers="Count" class="gt_row gt_right gt_striped">60</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.136</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA damage response</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">30.391</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">151</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.930</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">mitotic cell cycle process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">30.295</td>
## <td headers="Count" class="gt_row gt_right gt_striped">124</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.368</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome organization</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">27.626</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">103</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.307</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear division</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">26.108</td>
## <td headers="Count" class="gt_row gt_right gt_striped">80</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.535</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">nuclear chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">24.428</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">62</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.532</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organelle fission</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">23.724</td>
## <td headers="Count" class="gt_row gt_right gt_striped">83</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.440</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to chemokine</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.795</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">chemokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.795</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to chemokine</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.795</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">granulocyte chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">neutrophil chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.526</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">granulocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.523</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">leukocyte chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.523</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">neutrophil migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.523</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">L-phenylalanine catabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">L-phenylalanine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">alpha-amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.070</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.070</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">antimicrobial humoral immune response mediated by antimicrobial peptide</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.340</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">arachidonate transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">arachidonic acid secretion</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">carboxylic acid transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.378</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cell chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cellular response to cytokine stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cytokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">endothelial to hematopoietic transition</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.754</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">erythrose 4-phosphate/phosphoenolpyruvate family amino acid catabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">icosanoid secretion</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">icosanoid transport</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">inflammatory response</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">leukocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">myeloid leukocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">organic acid transport</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.378</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organic anion transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.378</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">polyamine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.730</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">positive regulation of wound healing</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.754</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of blood coagulation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.754</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">regulation of hemostasis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.754</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of neural retina development</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.621</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to cytokine</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">taxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">tyrosine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">41.099</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">88</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.140</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">40.741</td>
## <td headers="Count" class="gt_row gt_right gt_striped">140</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.898</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA damage response</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">37.952</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">160</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.848</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA-templated DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">35.898</td>
## <td headers="Count" class="gt_row gt_right gt_striped">63</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.153</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">33.055</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">91</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.647</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">chromosome organization</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">32.854</td>
## <td headers="Count" class="gt_row gt_right gt_striped">108</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.362</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">mitotic cell cycle process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">30.759</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">122</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.402</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear division</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">27.337</td>
## <td headers="Count" class="gt_row gt_right gt_striped">80</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.561</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">organelle fission</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.691</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">84</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.425</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">25.468</td>
## <td headers="Count" class="gt_row gt_right gt_striped">62</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.739</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to estrogen stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">11.573</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to estrogen</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">11.573</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−9.231</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to estradiol</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">11.015</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.270</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to lipid</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">6.552</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.304</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to hormone stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.376</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">lipid transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.844</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.837</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to hormone</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.844</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to organic cyclic compound</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.812</td>
## <td headers="Count" class="gt_row gt_right gt_striped">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−9.270</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">lipid localization</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.777</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−8.837</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to oxygen-containing compound</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">4.495</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.304</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">36.852</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">74</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.983</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">36.170</td>
## <td headers="Count" class="gt_row gt_right gt_striped">65</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.703</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">mitotic cell cycle process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">36.170</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">96</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.900</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">29.184</td>
## <td headers="Count" class="gt_row gt_right gt_striped">52</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.031</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome organization</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">28.831</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">76</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.837</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear division</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">27.500</td>
## <td headers="Count" class="gt_row gt_right gt_striped">61</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.946</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">sister chromatid segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">26.900</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">43</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.978</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organelle fission</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">25.799</td>
## <td headers="Count" class="gt_row gt_right gt_striped">63</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.895</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA-templated DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.586</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">43</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.777</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">mitotic sister chromatid segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">23.570</td>
## <td headers="Count" class="gt_row gt_right gt_striped">38</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.047</td></tr>
## </tbody>
##
##
## </table>
## </div>
##
## $All_Treatments_KEGG
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## <thead>
## <tr class="gt_heading">
## <td colspan="5" class="gt_heading gt_title gt_font_normal" style>Top KEGG Pathways - All_Treatments</td>
## </tr>
## <tr class="gt_heading">
## <td colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style>Pathway enrichment (top 10 per contrast)</td>
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## <tr class="gt_col_headings">
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Treatment Comparison">Treatment Comparison</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="KEGG Pathway">KEGG Pathway</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="-log10(adj p-value)">-log10(adj p-value)</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Gene Count">Gene Count</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Mean log2FC">Mean log2FC</th>
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## </thead>
## <tbody class="gt_table_body">
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">26.277</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">30</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.993</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cell cycle</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">26.007</td>
## <td headers="Count" class="gt_row gt_right gt_striped">63</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.012</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Mismatch repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">14.304</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">17</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.748</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Homologous recombination</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">14.148</td>
## <td headers="Count" class="gt_row gt_right gt_striped">22</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.889</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Fanconi anemia pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">9.354</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">20</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.078</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">PPAR signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">8.502</td>
## <td headers="Count" class="gt_row gt_right gt_striped">26</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.268</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Base excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.112</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">16</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.792</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">FoxO signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.928</td>
## <td headers="Count" class="gt_row gt_right gt_striped">33</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−0.250</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Nucleotide excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.625</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">17</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.775</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Apoptosis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.402</td>
## <td headers="Count" class="gt_row gt_right gt_striped">34</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">0.474</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">p53 signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.402</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">21</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">0.495</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">NOD-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.914</td>
## <td headers="Count" class="gt_row gt_right gt_striped">5</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.313</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">RIG-I-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">3.914</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.309</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Herpes simplex virus 1 infection</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.777</td>
## <td headers="Count" class="gt_row gt_right gt_striped">5</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−7.243</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Toll-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">3.605</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.535</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Apoptosis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">3</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.431</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cytokine-cytokine receptor interaction</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.526</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">3</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.422</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cytosolic DNA-sensing pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.699</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">C-type lectin receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.049</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.372</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cell cycle</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">26.135</td>
## <td headers="Count" class="gt_row gt_right gt_striped">73</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.270</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">22.544</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">30</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.015</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Mismatch repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">15.314</td>
## <td headers="Count" class="gt_row gt_right gt_striped">19</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.882</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Homologous recombination</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">13.636</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.036</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Fanconi anemia pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">12.606</td>
## <td headers="Count" class="gt_row gt_right gt_striped">26</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.121</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Drug metabolism - other enzymes</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.972</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">32</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−0.879</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">PPAR signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.673</td>
## <td headers="Count" class="gt_row gt_right gt_striped">29</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.527</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Base excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.507</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">20</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.782</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Drug metabolism - cytochrome P450</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">6.812</td>
## <td headers="Count" class="gt_row gt_right gt_striped">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.723</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Retinol metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.872</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">26</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.511</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Linoleic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Phenylalanine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.262</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Primary bile acid biosynthesis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.270</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Ubiquinone and other terpenoid-quinone biosynthesis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.262</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">alpha-Linolenic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Arachidonic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Arginine and proline metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.730</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cysteine and methionine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Ether lipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Glutathione metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.730</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Tyrosine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">28.698</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">34</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.996</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cell cycle</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">27.177</td>
## <td headers="Count" class="gt_row gt_right gt_striped">75</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.317</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Homologous recombination</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">14.390</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">25</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.161</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Mismatch repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">13.479</td>
## <td headers="Count" class="gt_row gt_right gt_striped">18</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.039</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Fanconi anemia pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">13.309</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">27</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.180</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Base excision repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">12.892</td>
## <td headers="Count" class="gt_row gt_right gt_striped">26</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.610</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">PPAR signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">12.527</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">36</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.403</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Proteasome</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">8.327</td>
## <td headers="Count" class="gt_row gt_right gt_striped">23</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.305</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Nucleotide excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.055</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">22</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.758</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Apoptosis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">6.211</td>
## <td headers="Count" class="gt_row gt_right gt_striped">44</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">0.543</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">FoxO signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.211</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">41</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">0.010</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Glycerolipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.877</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.896</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Glycerophospholipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.776</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.896</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Folate transport and metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.222</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.609</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Protein export</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.222</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.277</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">RNA polymerase</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.222</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.415</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">One carbon pool by folate</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.213</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.609</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cytosolic DNA-sensing pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.078</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.415</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cell cycle</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.694</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">54</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.848</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">20.877</td>
## <td headers="Count" class="gt_row gt_right gt_striped">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.671</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Mismatch repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">8.846</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.708</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Homologous recombination</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.418</td>
## <td headers="Count" class="gt_row gt_right gt_striped">14</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.756</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Fanconi anemia pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.917</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">15</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.918</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">PPAR signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.354</td>
## <td headers="Count" class="gt_row gt_right gt_striped">18</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.483</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Nucleotide excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.151</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">14</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.554</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">FoxO signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">4.314</td>
## <td headers="Count" class="gt_row gt_right gt_striped">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−0.288</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">p53 signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">4.265</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">16</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">0.420</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Base excision repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.862</td>
## <td headers="Count" class="gt_row gt_right gt_striped">11</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.612</td></tr>
## </tbody>
##
##
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## <thead>
## <tr class="gt_heading">
## <td colspan="5" class="gt_heading gt_title gt_font_normal" style>Top GO Terms - Parasite_Effect</td>
## </tr>
## <tr class="gt_heading">
## <td colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style>Biological Process enrichment (top 10 per contrast)</td>
## </tr>
## <tr class="gt_col_headings">
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Treatment Comparison">Treatment Comparison</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="GO Term">GO Term</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="-log10(adj p-value)">-log10(adj p-value)</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Gene Count">Gene Count</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Mean log2FC">Mean log2FC</th>
## </tr>
## </thead>
## <tbody class="gt_table_body">
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">36.852</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">74</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.983</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">36.170</td>
## <td headers="Count" class="gt_row gt_right gt_striped">65</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.703</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">mitotic cell cycle process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">36.170</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">96</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.900</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">29.184</td>
## <td headers="Count" class="gt_row gt_right gt_striped">52</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.031</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome organization</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">28.831</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">76</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.837</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear division</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">27.500</td>
## <td headers="Count" class="gt_row gt_right gt_striped">61</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.946</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">sister chromatid segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">26.900</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">43</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.978</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organelle fission</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">25.799</td>
## <td headers="Count" class="gt_row gt_right gt_striped">63</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.895</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA-templated DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.586</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">43</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.777</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">mitotic sister chromatid segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">23.570</td>
## <td headers="Count" class="gt_row gt_right gt_striped">38</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.047</td></tr>
## </tbody>
##
##
## </table>
## </div>
##
## $Parasite_Effect_KEGG
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## <td colspan="5" class="gt_heading gt_title gt_font_normal" style>Top KEGG Pathways - Parasite_Effect</td>
## </tr>
## <tr class="gt_heading">
## <td colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style>Pathway enrichment (top 10 per contrast)</td>
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## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Treatment Comparison">Treatment Comparison</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="KEGG Pathway">KEGG Pathway</th>
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## <tbody class="gt_table_body">
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cell cycle</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.694</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">54</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.848</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">20.877</td>
## <td headers="Count" class="gt_row gt_right gt_striped">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.671</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Mismatch repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">8.846</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.708</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Homologous recombination</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.418</td>
## <td headers="Count" class="gt_row gt_right gt_striped">14</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.756</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Fanconi anemia pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.917</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">15</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.918</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">PPAR signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.354</td>
## <td headers="Count" class="gt_row gt_right gt_striped">18</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.483</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Nucleotide excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.151</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">14</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.554</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">FoxO signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">4.314</td>
## <td headers="Count" class="gt_row gt_right gt_striped">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−0.288</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">p53 signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">4.265</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">16</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">0.420</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Base excision repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.862</td>
## <td headers="Count" class="gt_row gt_right gt_striped">11</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.612</td></tr>
## </tbody>
##
##
## </table>
## </div>
##
## $Historical_Contingency_GO
## <div id="ddvrmedbxr" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
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##
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## #ddvrmedbxr .gt_table {
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## border-top-width: 2px;
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## border-left-width: 2px;
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## display: inline-block;
## width: 100%;
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##
## #ddvrmedbxr .gt_spanner_row {
## border-bottom-style: hidden;
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## border-left-width: 1px;
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## border-right-width: 1px;
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## border-bottom-width: 2px;
## border-bottom-color: #D3D3D3;
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##
## #ddvrmedbxr .gt_from_md > :first-child {
## margin-top: 0;
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##
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##
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## padding-bottom: 8px;
## padding-left: 5px;
## padding-right: 5px;
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## border-top-style: none;
## border-top-width: 1px;
## border-top-color: #D3D3D3;
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## border-left-width: 1px;
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## border-right-width: 1px;
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##
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##
## #ddvrmedbxr .gt_stub_row_group {
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##
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## padding-bottom: 8px;
## padding-left: 5px;
## padding-right: 5px;
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##
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## border-top-color: #D3D3D3;
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##
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##
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## padding-bottom: 8px;
## padding-left: 5px;
## padding-right: 5px;
## border-bottom-style: none;
## border-bottom-width: 2px;
## border-bottom-color: #D3D3D3;
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##
## #ddvrmedbxr .gt_grand_summary_row {
## color: #333333;
## background-color: #FFFFFF;
## text-transform: inherit;
## padding-top: 8px;
## padding-bottom: 8px;
## padding-left: 5px;
## padding-right: 5px;
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##
## #ddvrmedbxr .gt_first_grand_summary_row {
## padding-top: 8px;
## padding-bottom: 8px;
## padding-left: 5px;
## padding-right: 5px;
## border-top-style: none;
## border-top-width: 6px;
## border-top-color: #D3D3D3;
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##
## #ddvrmedbxr .gt_last_grand_summary_row_top {
## padding-top: 8px;
## padding-bottom: 8px;
## padding-left: 5px;
## padding-right: 5px;
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## border-bottom-color: #D3D3D3;
## }
##
## #ddvrmedbxr .gt_striped {
## background-color: rgba(128, 128, 128, 0.05);
## }
##
## #ddvrmedbxr .gt_table_body {
## border-top-style: none;
## border-top-width: 2px;
## border-top-color: #D3D3D3;
## border-bottom-style: none;
## border-bottom-width: 2px;
## border-bottom-color: #D3D3D3;
## }
##
## #ddvrmedbxr .gt_footnotes {
## color: #333333;
## background-color: #FFFFFF;
## border-bottom-style: none;
## border-bottom-width: 2px;
## border-bottom-color: #D3D3D3;
## border-left-style: none;
## border-left-width: 2px;
## border-left-color: #D3D3D3;
## border-right-style: none;
## border-right-width: 2px;
## border-right-color: #D3D3D3;
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##
## #ddvrmedbxr .gt_footnote {
## margin: 0px;
## font-size: 90%;
## padding-top: 4px;
## padding-bottom: 4px;
## padding-left: 5px;
## padding-right: 5px;
## }
##
## #ddvrmedbxr .gt_sourcenotes {
## color: #333333;
## background-color: #FFFFFF;
## border-bottom-style: none;
## border-bottom-width: 2px;
## border-bottom-color: #D3D3D3;
## border-left-style: none;
## border-left-width: 2px;
## border-left-color: #D3D3D3;
## border-right-style: none;
## border-right-width: 2px;
## border-right-color: #D3D3D3;
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##
## #ddvrmedbxr .gt_sourcenote {
## font-size: 90%;
## padding-top: 4px;
## padding-bottom: 4px;
## padding-left: 5px;
## padding-right: 5px;
## }
##
## #ddvrmedbxr .gt_left {
## text-align: left;
## }
##
## #ddvrmedbxr .gt_center {
## text-align: center;
## }
##
## #ddvrmedbxr .gt_right {
## text-align: right;
## font-variant-numeric: tabular-nums;
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##
## #ddvrmedbxr .gt_font_normal {
## font-weight: normal;
## }
##
## #ddvrmedbxr .gt_font_bold {
## font-weight: bold;
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##
## #ddvrmedbxr .gt_font_italic {
## font-style: italic;
## }
##
## #ddvrmedbxr .gt_super {
## font-size: 65%;
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##
## #ddvrmedbxr .gt_footnote_marks {
## font-size: 75%;
## vertical-align: 0.4em;
## position: initial;
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##
## #ddvrmedbxr .gt_asterisk {
## font-size: 100%;
## vertical-align: 0;
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##
## #ddvrmedbxr .gt_indent_1 {
## text-indent: 5px;
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##
## #ddvrmedbxr .gt_indent_2 {
## text-indent: 10px;
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##
## #ddvrmedbxr .gt_indent_3 {
## text-indent: 15px;
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##
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## text-indent: 20px;
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##
## #ddvrmedbxr .gt_indent_5 {
## text-indent: 25px;
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## </style>
## <table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
## <thead>
## <tr class="gt_heading">
## <td colspan="5" class="gt_heading gt_title gt_font_normal" style>Top GO Terms - Historical_Contingency</td>
## </tr>
## <tr class="gt_heading">
## <td colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style>Biological Process enrichment (top 10 per contrast)</td>
## </tr>
## <tr class="gt_col_headings">
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Treatment Comparison">Treatment Comparison</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="GO Term">GO Term</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="-log10(adj p-value)">-log10(adj p-value)</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Gene Count">Gene Count</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Mean log2FC">Mean log2FC</th>
## </tr>
## </thead>
## <tbody class="gt_table_body">
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">acrosome reaction</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.215</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">3.216</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">apoptotic signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.215</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.223</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cell-cell adhesion via plasma-membrane adhesion molecules</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.215</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.567</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">egg coat formation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.215</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">3.216</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">homophilic cell adhesion via plasma membrane adhesion molecules</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.215</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.567</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">positive regulation of acrosome reaction</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.215</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">3.216</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of acrosome reaction</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.215</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">3.216</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">binding of sperm to zona pellucida</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.173</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">3.216</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular modified amino acid biosynthetic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.173</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.540</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.173</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.993</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">sperm-egg recognition</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.173</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">3.216</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">actomyosin structure organization</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.385</td>
## <td headers="Count" class="gt_row gt_right gt_striped">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.032</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of reactive oxygen species metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.385</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.697</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">one-carbon compound transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.022</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.215</td></tr>
## </tbody>
##
##
## </table>
## </div>
##
## $Historical_Contingency_KEGG
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## <td colspan="5" class="gt_heading gt_title gt_font_normal" style>Top KEGG Pathways - Historical_Contingency</td>
## </tr>
## <tr class="gt_heading">
## <td colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style>Pathway enrichment (top 10 per contrast)</td>
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## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Treatment Comparison">Treatment Comparison</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="KEGG Pathway">KEGG Pathway</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="-log10(adj p-value)">-log10(adj p-value)</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Gene Count">Gene Count</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Mean log2FC">Mean log2FC</th>
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## </thead>
## <tbody class="gt_table_body">
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Arginine and proline metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.953</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.540</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cytoskeleton in muscle cells</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.560</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.540</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Drug metabolism - cytochrome P450</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.871</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.293</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Metabolism of xenobiotics by cytochrome P450</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.871</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.293</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Drug metabolism - other enzymes</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.744</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.293</td></tr>
## </tbody>
##
##
## </table>
## </div>
##
## $Recovery_Analysis_GO
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## <table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
## <thead>
## <tr class="gt_heading">
## <td colspan="5" class="gt_heading gt_title gt_font_normal" style>Top GO Terms - Recovery_Analysis</td>
## </tr>
## <tr class="gt_heading">
## <td colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style>Biological Process enrichment (top 10 per contrast)</td>
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## <tr class="gt_col_headings">
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Treatment Comparison">Treatment Comparison</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="GO Term">GO Term</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="-log10(adj p-value)">-log10(adj p-value)</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Gene Count">Gene Count</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Mean log2FC">Mean log2FC</th>
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## </thead>
## <tbody class="gt_table_body">
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">8.202</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">13</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.390</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to virus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">8.202</td>
## <td headers="Count" class="gt_row gt_right gt_striped">8</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.820</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response to other organism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.622</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">11</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.700</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to biotic stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.622</td>
## <td headers="Count" class="gt_row gt_right gt_striped">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.653</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to external biotic stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.622</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.653</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to other organism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.622</td>
## <td headers="Count" class="gt_row gt_right gt_striped">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.653</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response to symbiont</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.901</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.735</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">defense response to virus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.901</td>
## <td headers="Count" class="gt_row gt_right gt_striped">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.735</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cytokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.734</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.223</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cellular response to cytokine stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.700</td>
## <td headers="Count" class="gt_row gt_right gt_striped">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.223</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to chemokine</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.795</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">chemokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.795</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to chemokine</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.795</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">granulocyte chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">neutrophil chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.526</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">granulocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.523</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">leukocyte chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.523</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">neutrophil migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.523</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">L-phenylalanine catabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">L-phenylalanine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">alpha-amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.070</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.070</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">antimicrobial humoral immune response mediated by antimicrobial peptide</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.340</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">arachidonate transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">arachidonic acid secretion</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">carboxylic acid transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.378</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cell chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cellular response to cytokine stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cytokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">endothelial to hematopoietic transition</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.754</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">erythrose 4-phosphate/phosphoenolpyruvate family amino acid catabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">icosanoid secretion</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">icosanoid transport</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">inflammatory response</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">leukocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">myeloid leukocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">organic acid transport</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.378</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organic anion transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.378</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">polyamine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.730</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">positive regulation of wound healing</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.754</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of blood coagulation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.754</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">regulation of hemostasis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.754</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of neural retina development</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.621</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to cytokine</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">taxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">tyrosine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to estrogen stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">11.573</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to estrogen</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">11.573</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−9.231</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to estradiol</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">11.015</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.270</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to lipid</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">6.552</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.304</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to hormone stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.376</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">lipid transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.844</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.837</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to hormone</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.844</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to organic cyclic compound</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.812</td>
## <td headers="Count" class="gt_row gt_right gt_striped">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−9.270</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">lipid localization</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.777</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−8.837</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to oxygen-containing compound</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">4.495</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.304</td></tr>
## </tbody>
##
##
## </table>
## </div>
##
## $Recovery_Analysis_KEGG
## <div id="eaqgdmjilt" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
## <style>#eaqgdmjilt table {
## font-family: Arial, system-ui, 'Segoe UI', Roboto, Helvetica, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji';
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## <thead>
## <tr class="gt_heading">
## <td colspan="5" class="gt_heading gt_title gt_font_normal" style>Top KEGG Pathways - Recovery_Analysis</td>
## </tr>
## <tr class="gt_heading">
## <td colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style>Pathway enrichment (top 10 per contrast)</td>
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## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Treatment Comparison">Treatment Comparison</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="KEGG Pathway">KEGG Pathway</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="-log10(adj p-value)">-log10(adj p-value)</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Gene Count">Gene Count</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Mean log2FC">Mean log2FC</th>
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## <tbody class="gt_table_body">
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">NOD-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">3.914</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">5</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.313</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">RIG-I-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.914</td>
## <td headers="Count" class="gt_row gt_right gt_striped">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.309</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Herpes simplex virus 1 infection</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">3.777</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">5</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−7.243</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Toll-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.605</td>
## <td headers="Count" class="gt_row gt_right gt_striped">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.535</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Apoptosis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.526</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">3</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.431</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cytokine-cytokine receptor interaction</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">3</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.422</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cytosolic DNA-sensing pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.526</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.699</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">C-type lectin receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.049</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.372</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Linoleic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.262</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Phenylalanine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Primary bile acid biosynthesis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.262</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.270</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Ubiquinone and other terpenoid-quinone biosynthesis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">alpha-Linolenic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.262</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Arachidonic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Arginine and proline metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.730</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cysteine and methionine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Ether lipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Glutathione metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.730</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Tyrosine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Glycerolipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.877</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.896</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Glycerophospholipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.776</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.896</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Folate transport and metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.222</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.609</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Protein export</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.222</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.277</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">RNA polymerase</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.222</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.415</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">One carbon pool by folate</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.213</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.609</td></tr>
## <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cytosolic DNA-sensing pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.078</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.415</td></tr>
## </tbody>
##
##
## </table>
## </div>
##
## $Combined_GO
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## <tr class="gt_heading">
## <td colspan="6" class="gt_heading gt_title gt_font_normal" style>Combined GO Terms Summary</td>
## </tr>
## <tr class="gt_heading">
## <td colspan="6" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style>Top enriched biological processes across all analyses</td>
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## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Analysis">Analysis</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Treatment Comparison">Treatment Comparison</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="GO Term">GO Term</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="-log10(adj p-value)">-log10(adj p-value)</th>
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## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">43.746</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">82</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.963</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">mitotic cell cycle process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">35.875</td>
## <td headers="Count" class="gt_row gt_right gt_striped">114</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.204</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA-templated DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">33.442</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">56</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.020</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">chromosome organization</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">31.704</td>
## <td headers="Count" class="gt_row gt_right gt_striped">94</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.083</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">31.165</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">79</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.272</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear division</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">28.063</td>
## <td headers="Count" class="gt_row gt_right gt_striped">72</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.269</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">27.219</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">104</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.964</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA damage response</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">27.194</td>
## <td headers="Count" class="gt_row gt_right gt_striped">122</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.901</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">nuclear chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.738</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">56</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.292</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organelle fission</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">25.633</td>
## <td headers="Count" class="gt_row gt_right gt_striped">74</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.219</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">8.202</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">13</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.390</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to virus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">8.202</td>
## <td headers="Count" class="gt_row gt_right gt_striped">8</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.820</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response to other organism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.622</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">11</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.700</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to biotic stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.622</td>
## <td headers="Count" class="gt_row gt_right gt_striped">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.653</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to external biotic stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.622</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.653</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to other organism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.622</td>
## <td headers="Count" class="gt_row gt_right gt_striped">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.653</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response to symbiont</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.901</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.735</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">defense response to virus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.901</td>
## <td headers="Count" class="gt_row gt_right gt_striped">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.735</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cytokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.734</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.223</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cellular response to cytokine stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.700</td>
## <td headers="Count" class="gt_row gt_right gt_striped">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.223</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">36.497</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">85</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.148</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">32.107</td>
## <td headers="Count" class="gt_row gt_right gt_striped">92</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.423</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">31.115</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">129</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.005</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA-templated DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">31.074</td>
## <td headers="Count" class="gt_row gt_right gt_striped">60</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.136</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA damage response</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">30.391</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">151</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.930</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">mitotic cell cycle process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">30.295</td>
## <td headers="Count" class="gt_row gt_right gt_striped">124</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.368</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome organization</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">27.626</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">103</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.307</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear division</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">26.108</td>
## <td headers="Count" class="gt_row gt_right gt_striped">80</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.535</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">nuclear chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">24.428</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">62</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.532</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organelle fission</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">23.724</td>
## <td headers="Count" class="gt_row gt_right gt_striped">83</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.440</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to chemokine</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.795</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">chemokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.795</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to chemokine</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.795</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">granulocyte chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">neutrophil chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.526</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">granulocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.523</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">leukocyte chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.523</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">neutrophil migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.523</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">L-phenylalanine catabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">L-phenylalanine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">alpha-amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.070</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.070</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">antimicrobial humoral immune response mediated by antimicrobial peptide</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.340</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">arachidonate transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">arachidonic acid secretion</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">carboxylic acid transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.378</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cell chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cellular response to cytokine stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cytokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">endothelial to hematopoietic transition</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.754</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">erythrose 4-phosphate/phosphoenolpyruvate family amino acid catabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">icosanoid secretion</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">icosanoid transport</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">inflammatory response</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">leukocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">myeloid leukocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">organic acid transport</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.378</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organic anion transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.378</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">polyamine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.730</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">positive regulation of wound healing</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.754</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of blood coagulation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.754</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">regulation of hemostasis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.754</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of neural retina development</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.621</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to cytokine</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">taxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">tyrosine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">41.099</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">88</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.140</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">40.741</td>
## <td headers="Count" class="gt_row gt_right gt_striped">140</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.898</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA damage response</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">37.952</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">160</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.848</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA-templated DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">35.898</td>
## <td headers="Count" class="gt_row gt_right gt_striped">63</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.153</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">33.055</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">91</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.647</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">chromosome organization</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">32.854</td>
## <td headers="Count" class="gt_row gt_right gt_striped">108</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.362</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">mitotic cell cycle process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">30.759</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">122</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.402</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear division</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">27.337</td>
## <td headers="Count" class="gt_row gt_right gt_striped">80</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.561</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">organelle fission</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.691</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">84</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.425</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">25.468</td>
## <td headers="Count" class="gt_row gt_right gt_striped">62</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.739</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to estrogen stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">11.573</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to estrogen</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">11.573</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−9.231</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to estradiol</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">11.015</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.270</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to lipid</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">6.552</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.304</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to hormone stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.376</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">lipid transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.844</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.837</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to hormone</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.844</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to organic cyclic compound</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.812</td>
## <td headers="Count" class="gt_row gt_right gt_striped">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−9.270</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">lipid localization</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.777</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−8.837</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to oxygen-containing compound</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">4.495</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.304</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">36.852</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">74</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.983</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">36.170</td>
## <td headers="Count" class="gt_row gt_right gt_striped">65</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.703</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">mitotic cell cycle process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">36.170</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">96</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.900</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">29.184</td>
## <td headers="Count" class="gt_row gt_right gt_striped">52</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.031</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome organization</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">28.831</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">76</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.837</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear division</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">27.500</td>
## <td headers="Count" class="gt_row gt_right gt_striped">61</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.946</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">sister chromatid segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">26.900</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">43</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.978</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organelle fission</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">25.799</td>
## <td headers="Count" class="gt_row gt_right gt_striped">63</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.895</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA-templated DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.586</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">43</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.777</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">mitotic sister chromatid segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">23.570</td>
## <td headers="Count" class="gt_row gt_right gt_striped">38</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.047</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">acrosome reaction</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.215</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">3.216</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">apoptotic signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.215</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.223</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cell-cell adhesion via plasma-membrane adhesion molecules</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.215</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.567</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">egg coat formation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.215</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">3.216</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">homophilic cell adhesion via plasma membrane adhesion molecules</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.215</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.567</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">positive regulation of acrosome reaction</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.215</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">3.216</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of acrosome reaction</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.215</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">3.216</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">binding of sperm to zona pellucida</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.173</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">3.216</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular modified amino acid biosynthetic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.173</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.540</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.173</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.993</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">sperm-egg recognition</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.173</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">3.216</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">actomyosin structure organization</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.385</td>
## <td headers="Count" class="gt_row gt_right gt_striped">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.032</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of reactive oxygen species metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.385</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.697</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">one-carbon compound transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.022</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.215</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">36.852</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">74</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.983</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">36.170</td>
## <td headers="Count" class="gt_row gt_right gt_striped">65</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.703</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">mitotic cell cycle process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">36.170</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">96</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.900</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">29.184</td>
## <td headers="Count" class="gt_row gt_right gt_striped">52</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.031</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome organization</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">28.831</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">76</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.837</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear division</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">27.500</td>
## <td headers="Count" class="gt_row gt_right gt_striped">61</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.946</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">sister chromatid segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">26.900</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">43</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.978</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organelle fission</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">25.799</td>
## <td headers="Count" class="gt_row gt_right gt_striped">63</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.895</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA-templated DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.586</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">43</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.777</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">mitotic sister chromatid segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">23.570</td>
## <td headers="Count" class="gt_row gt_right gt_striped">38</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.047</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">8.202</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">13</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.390</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to virus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">8.202</td>
## <td headers="Count" class="gt_row gt_right gt_striped">8</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.820</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response to other organism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.622</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">11</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.700</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to biotic stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.622</td>
## <td headers="Count" class="gt_row gt_right gt_striped">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.653</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to external biotic stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.622</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.653</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to other organism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.622</td>
## <td headers="Count" class="gt_row gt_right gt_striped">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.653</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response to symbiont</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.901</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.735</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">defense response to virus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.901</td>
## <td headers="Count" class="gt_row gt_right gt_striped">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.735</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cytokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.734</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.223</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cellular response to cytokine stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.700</td>
## <td headers="Count" class="gt_row gt_right gt_striped">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.223</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to chemokine</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.795</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">chemokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.795</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to chemokine</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.795</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">granulocyte chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">neutrophil chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.526</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">granulocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.523</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">leukocyte chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.523</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">neutrophil migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.523</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">L-phenylalanine catabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">L-phenylalanine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">alpha-amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.070</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.070</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">antimicrobial humoral immune response mediated by antimicrobial peptide</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.340</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">arachidonate transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">arachidonic acid secretion</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">carboxylic acid transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.378</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cell chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cellular response to cytokine stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cytokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">endothelial to hematopoietic transition</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.754</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">erythrose 4-phosphate/phosphoenolpyruvate family amino acid catabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">icosanoid secretion</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">icosanoid transport</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">inflammatory response</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">leukocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">myeloid leukocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">organic acid transport</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.378</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organic anion transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.378</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">polyamine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.730</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">positive regulation of wound healing</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.754</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of blood coagulation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.754</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">regulation of hemostasis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.754</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of neural retina development</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.621</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to cytokine</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">taxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">tyrosine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to estrogen stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">11.573</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to estrogen</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">11.573</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−9.231</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to estradiol</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">11.015</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.270</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to lipid</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">6.552</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.304</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to hormone stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.376</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">lipid transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.844</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.837</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to hormone</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.844</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to organic cyclic compound</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.812</td>
## <td headers="Count" class="gt_row gt_right gt_striped">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−9.270</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">lipid localization</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.777</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−8.837</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to oxygen-containing compound</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">4.495</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.304</td></tr>
## </tbody>
##
##
## </table>
## </div>
##
## $Combined_KEGG
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## <thead>
## <tr class="gt_heading">
## <td colspan="6" class="gt_heading gt_title gt_font_normal" style>Combined KEGG Pathways Summary</td>
## </tr>
## <tr class="gt_heading">
## <td colspan="6" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style>Top enriched pathways across all analyses</td>
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## <tr class="gt_col_headings">
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Analysis">Analysis</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Treatment Comparison">Treatment Comparison</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="KEGG Pathway">KEGG Pathway</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="-log10(adj p-value)">-log10(adj p-value)</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Gene Count">Gene Count</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Mean log2FC">Mean log2FC</th>
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## <tbody class="gt_table_body">
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">26.277</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">30</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.993</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cell cycle</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">26.007</td>
## <td headers="Count" class="gt_row gt_right gt_striped">63</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.012</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Mismatch repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">14.304</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">17</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.748</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Homologous recombination</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">14.148</td>
## <td headers="Count" class="gt_row gt_right gt_striped">22</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.889</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Fanconi anemia pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">9.354</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">20</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.078</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">PPAR signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">8.502</td>
## <td headers="Count" class="gt_row gt_right gt_striped">26</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.268</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Base excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.112</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">16</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.792</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">FoxO signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.928</td>
## <td headers="Count" class="gt_row gt_right gt_striped">33</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−0.250</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Nucleotide excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.625</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">17</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.775</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Apoptosis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.402</td>
## <td headers="Count" class="gt_row gt_right gt_striped">34</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">0.474</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">p53 signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.402</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">21</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">0.495</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">NOD-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.914</td>
## <td headers="Count" class="gt_row gt_right gt_striped">5</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.313</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">RIG-I-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">3.914</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.309</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Herpes simplex virus 1 infection</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.777</td>
## <td headers="Count" class="gt_row gt_right gt_striped">5</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−7.243</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Toll-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">3.605</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.535</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Apoptosis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">3</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.431</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cytokine-cytokine receptor interaction</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.526</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">3</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.422</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cytosolic DNA-sensing pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.699</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">C-type lectin receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.049</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.372</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cell cycle</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">26.135</td>
## <td headers="Count" class="gt_row gt_right gt_striped">73</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.270</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">22.544</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">30</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.015</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Mismatch repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">15.314</td>
## <td headers="Count" class="gt_row gt_right gt_striped">19</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.882</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Homologous recombination</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">13.636</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.036</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Fanconi anemia pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">12.606</td>
## <td headers="Count" class="gt_row gt_right gt_striped">26</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.121</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Drug metabolism - other enzymes</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.972</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">32</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−0.879</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">PPAR signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.673</td>
## <td headers="Count" class="gt_row gt_right gt_striped">29</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.527</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Base excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.507</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">20</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.782</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Drug metabolism - cytochrome P450</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">6.812</td>
## <td headers="Count" class="gt_row gt_right gt_striped">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.723</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Retinol metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.872</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">26</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.511</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Linoleic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Phenylalanine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.262</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Primary bile acid biosynthesis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.270</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Ubiquinone and other terpenoid-quinone biosynthesis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.262</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">alpha-Linolenic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Arachidonic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Arginine and proline metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.730</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cysteine and methionine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Ether lipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Glutathione metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.730</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Tyrosine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">28.698</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">34</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.996</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cell cycle</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">27.177</td>
## <td headers="Count" class="gt_row gt_right gt_striped">75</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.317</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Homologous recombination</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">14.390</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">25</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.161</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Mismatch repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">13.479</td>
## <td headers="Count" class="gt_row gt_right gt_striped">18</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.039</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Fanconi anemia pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">13.309</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">27</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.180</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Base excision repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">12.892</td>
## <td headers="Count" class="gt_row gt_right gt_striped">26</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.610</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">PPAR signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">12.527</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">36</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.403</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Proteasome</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">8.327</td>
## <td headers="Count" class="gt_row gt_right gt_striped">23</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.305</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Nucleotide excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.055</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">22</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.758</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Apoptosis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">6.211</td>
## <td headers="Count" class="gt_row gt_right gt_striped">44</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">0.543</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">FoxO signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.211</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">41</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">0.010</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Glycerolipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.877</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.896</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Glycerophospholipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.776</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.896</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Folate transport and metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.222</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.609</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Protein export</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.222</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.277</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">RNA polymerase</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.222</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.415</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">One carbon pool by folate</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.213</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.609</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cytosolic DNA-sensing pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.078</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.415</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cell cycle</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.694</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">54</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.848</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">20.877</td>
## <td headers="Count" class="gt_row gt_right gt_striped">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.671</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Mismatch repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">8.846</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.708</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Homologous recombination</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.418</td>
## <td headers="Count" class="gt_row gt_right gt_striped">14</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.756</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Fanconi anemia pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.917</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">15</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.918</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">PPAR signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.354</td>
## <td headers="Count" class="gt_row gt_right gt_striped">18</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.483</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Nucleotide excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.151</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">14</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.554</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">FoxO signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">4.314</td>
## <td headers="Count" class="gt_row gt_right gt_striped">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−0.288</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">p53 signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">4.265</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">16</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">0.420</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Base excision repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.862</td>
## <td headers="Count" class="gt_row gt_right gt_striped">11</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.612</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Arginine and proline metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.953</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.540</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cytoskeleton in muscle cells</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.560</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.540</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Drug metabolism - cytochrome P450</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.871</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.293</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Metabolism of xenobiotics by cytochrome P450</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.871</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.293</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Drug metabolism - other enzymes</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.744</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.293</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cell cycle</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">25.694</td>
## <td headers="Count" class="gt_row gt_right gt_striped">54</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.848</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">20.877</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.671</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Mismatch repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">8.846</td>
## <td headers="Count" class="gt_row gt_right gt_striped">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.708</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Homologous recombination</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.418</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">14</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.756</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Fanconi anemia pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">6.917</td>
## <td headers="Count" class="gt_row gt_right gt_striped">15</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.918</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">PPAR signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.354</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">18</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.483</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Nucleotide excision repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.151</td>
## <td headers="Count" class="gt_row gt_right gt_striped">14</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.554</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">FoxO signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">4.314</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−0.288</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">p53 signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">4.265</td>
## <td headers="Count" class="gt_row gt_right gt_striped">16</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">0.420</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Base excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">3.862</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">11</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.612</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">NOD-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.914</td>
## <td headers="Count" class="gt_row gt_right gt_striped">5</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.313</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">RIG-I-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">3.914</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.309</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Herpes simplex virus 1 infection</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.777</td>
## <td headers="Count" class="gt_row gt_right gt_striped">5</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−7.243</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Toll-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">3.605</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.535</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Apoptosis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">3</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.431</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cytokine-cytokine receptor interaction</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.526</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">3</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.422</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cytosolic DNA-sensing pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.699</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">C-type lectin receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.049</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.372</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Linoleic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Phenylalanine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.262</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Primary bile acid biosynthesis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.270</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Ubiquinone and other terpenoid-quinone biosynthesis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.262</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">alpha-Linolenic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Arachidonic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Arginine and proline metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.730</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cysteine and methionine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Ether lipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Glutathione metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.730</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Tyrosine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Glycerolipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.877</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.896</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Glycerophospholipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.776</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.896</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Folate transport and metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.222</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.609</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Protein export</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.222</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.277</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">RNA polymerase</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.222</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.415</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">One carbon pool by folate</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.213</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.609</td></tr>
## <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cytosolic DNA-sensing pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.078</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.415</td></tr>
## </tbody>
##
##
## </table>
## </div>
sessionInfo()
## R version 4.3.3 (2024-02-29)
## Platform: x86_64-apple-darwin20 (64-bit)
## Running under: macOS 15.3
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: America/Los_Angeles
## tzcode source: internal
##
## attached base packages:
## [1] grid stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] furrr_0.3.1 future_1.33.2
## [3] org.Dr.eg.db_3.18.0 AnnotationDbi_1.64.1
## [5] clusterProfiler_4.10.1 coin_1.4-3
## [7] rstatix_0.7.2 multcomp_1.4-25
## [9] TH.data_1.1-2 MASS_7.3-60.0.1
## [11] survival_3.6-4 mvtnorm_1.2-5
## [13] emmeans_1.10.1 car_3.1-2
## [15] carData_3.0-5 broom_1.0.6
## [17] gt_0.10.1 BiocParallel_1.36.0
## [19] gridExtra_2.3 VennDiagram_1.7.3
## [21] futile.logger_1.4.3 lubridate_1.9.3
## [23] forcats_1.0.0 stringr_1.5.1
## [25] dplyr_1.1.4 purrr_1.0.2
## [27] readr_2.1.5 tidyr_1.3.1
## [29] tibble_3.2.1 tidyverse_2.0.0
## [31] ggrepel_0.9.5 RColorBrewer_1.1-3
## [33] pheatmap_1.0.12 ggplot2_3.5.1
## [35] DESeq2_1.42.1 SummarizedExperiment_1.32.0
## [37] Biobase_2.62.0 MatrixGenerics_1.14.0
## [39] matrixStats_1.3.0 GenomicRanges_1.54.1
## [41] GenomeInfoDb_1.38.8 IRanges_2.36.0
## [43] S4Vectors_0.40.2 BiocGenerics_0.48.1
##
## loaded via a namespace (and not attached):
## [1] splines_4.3.3 bitops_1.0-7 ggplotify_0.1.2
## [4] cellranger_1.1.0 polyclip_1.10-6 lifecycle_1.0.4
## [7] rprojroot_2.0.4 globals_0.16.3 lattice_0.22-6
## [10] backports_1.5.0 magrittr_2.0.3 sass_0.4.9
## [13] rmarkdown_2.26 jquerylib_0.1.4 yaml_2.3.8
## [16] cowplot_1.1.3 DBI_1.2.3 abind_1.4-5
## [19] zlibbioc_1.48.2 ggraph_2.2.1 RCurl_1.98-1.14
## [22] yulab.utils_0.2.0 tweenr_2.0.3 sandwich_3.1-0
## [25] GenomeInfoDbData_1.2.11 enrichplot_1.22.0 listenv_0.9.1
## [28] tidytree_0.4.6 parallelly_1.37.1 codetools_0.2-20
## [31] DelayedArray_0.28.0 DOSE_3.28.2 xml2_1.3.6
## [34] ggforce_0.4.2 tidyselect_1.2.1 aplot_0.2.3
## [37] farver_2.1.2 viridis_0.6.5 jsonlite_1.8.8
## [40] tidygraph_1.3.1 tools_4.3.3 treeio_1.26.0
## [43] Rcpp_1.0.12 glue_1.7.0 SparseArray_1.2.4
## [46] xfun_0.43 here_1.0.1 qvalue_2.34.0
## [49] withr_3.0.0 formatR_1.14 fastmap_1.2.0
## [52] fansi_1.0.6 digest_0.6.35 timechange_0.3.0
## [55] R6_2.5.1 gridGraphics_0.5-1 estimability_1.5
## [58] colorspace_2.1-0 GO.db_3.18.0 RSQLite_2.3.6
## [61] utf8_1.2.4 generics_0.1.3 data.table_1.15.4
## [64] graphlayouts_1.1.1 httr_1.4.7 S4Arrays_1.2.1
## [67] scatterpie_0.2.4 pkgconfig_2.0.3 gtable_0.3.5
## [70] modeltools_0.2-23 blob_1.2.4 XVector_0.42.0
## [73] shadowtext_0.1.4 htmltools_0.5.8.1 fgsea_1.28.0
## [76] scales_1.3.0 png_0.1-8 ggfun_0.1.5
## [79] knitr_1.45 lambda.r_1.2.4 rstudioapi_0.16.0
## [82] tzdb_0.4.0 reshape2_1.4.4 coda_0.19-4.1
## [85] nlme_3.1-164 cachem_1.1.0 zoo_1.8-12
## [88] parallel_4.3.3 HDO.db_0.99.1 libcoin_1.0-10
## [91] pillar_1.9.0 vctrs_0.6.5 xtable_1.8-4
## [94] evaluate_0.23 cli_3.6.2 locfit_1.5-9.9
## [97] compiler_4.3.3 futile.options_1.0.1 rlang_1.1.4
## [100] crayon_1.5.2 labeling_0.4.3 plyr_1.8.9
## [103] fs_1.6.4 stringi_1.8.4 viridisLite_0.4.2
## [106] munsell_0.5.1 Biostrings_2.70.3 lazyeval_0.2.2
## [109] GOSemSim_2.28.1 Matrix_1.6-5 hms_1.1.3
## [112] patchwork_1.2.0 bit64_4.0.5 KEGGREST_1.42.0
## [115] highr_0.10 igraph_2.0.3 memoise_2.0.1
## [118] bslib_0.7.0 ggtree_3.13.0.001 fastmatch_1.1-4
## [121] bit_4.0.5 readxl_1.4.3 gson_0.1.0
## [124] ape_5.8